System and method for outcome tracking and analysis

ABSTRACT

Provided are systems and methods for capturing outcome information associated with various cancer treatments. The system facilitates capture and analysis of cancer treatment information and associated outcome information. The treatment and outcome information can include genomic analysis and information on treatment of different cancers. The system can store and analyze any one or more of: tumor type, genomic alterations (e.g., genes and associated alterations, gene sequence mutations, alterations, amplifications, deletions, etc.), and treatment data (including, for example, treatments targeted to specific genes and/or genomic alterations). Users of the outcome system can supply and use the treatment and outcome information to facilitate diagnosis and therapy decisions. User interfaces within the system can be configured to allow users to easily locate outcome information associated with particular treatments of tumors having certain genomic alterations.

RELATED APPLICATIONS

This application is a non-provisional of and claims priority under 35U.S.C. §119(e) to U.S. Provisional App. No. 61/749,291, entitled “SYSTEMAND METHOD FOR MANAGING GENOMIC TESTING RESULTS,” filed Jan. 5, 2013,and U.S. Provisional App. No. 61/749,288, entitled “SYSTEM AND METHODFOR OUTCOME TRACKING AND ANALYSIS,” filed Jan. 5, 2013, whichapplications are incorporated herein by reference in their entirety.

BACKGROUND

Many conventional resources exist for accessing outcome informationassociated with patient populations and medical treatments. For example,cancer treatment information may be available through various resources.Notably, ClinicalTrials.gov provides public access to clinical trialsthrough search interfaces. The web site and interfaces enable searchingthrough registered trials based on keywords that can be input by a user.

SUMMARY

It is realized that conventional approaches and publically availableinformation sources fail to capture a large portion of outcomeinformation associated with medical treatments, including, for example,cancer treatment. Further, some conventional approaches fail to providevaluable information on the progression of treatment. In one example,some conventional approaches can fail to present changes in therapy overtime and the response of the disease over the various stages oftreatment. In other settings, conventional approaches can fail todistill treatment and outcome information into useable and/or actionableinformation that a physician can apply in daily practice or, in anotherexample, use to inform the physician's decision on potential treatmentoptions. In other instances, physicians and other health professionalsneed prior knowledge of multiple systems and knowledge of cancertreatments to obtain the necessary information to make an informedtreatment decision.

Accordingly, provided are systems and methods for capturing outcomeinformation associated with various cancer treatments. According to oneaspect, a system is provided that facilitates capture and analysis ofcancer treatment information and associated outcome information.According to one embodiment, cancer treatment information and outcomeinformation can include information relating to genetic analysis andtreatment of different cancers. In one embodiment, a system may beprovided that stores and analyzes a group of information including tumortype, genomic alterations (e.g., genes and associated alterations, genesequence mutations, alterations, amplifications, deletions, etc.), andtreatment (including, for example, treatments targeted to specific genesand/or genomic alterations). Users of the outcome system can supply anduse the treatment and outcome information to facilitate diagnosis andtherapy decisions. Such an outcome system may be accessed by usersthrough a user-facing application referred to herein as an outcomeapplication. Further, user interfaces of the outcome application may beprovided to easily allow users to locate outcome information associatedwith particular treatments of tumors having certain genomic alterations.

According to another embodiment of the present invention, genomicalteration data is correlated with outcome data, and tools are providedto allow users to easily locate such correlations. For instance, it maybe useful to have a tool that allows a physician to locate treatment andoutcome information for patients with the same or similar genomicalterations occurring in different tumor types to inform decision-makingfor off-label uses of a particular treatment. In another embodiment,contact information for treating physicians associated with particulartreatment/outcomes may be stored, and this contact information may beused by physicians or other personnel to contact such treatingphysicians for questions regarding their cases. This feature may permit,for example, socialization among physicians resulting in improvedpatient outcomes. In further embodiments, genomic testing informationcan be developed on the system, accessed, or requested. Genomic testscan be used to analyze a patient's cancer, specific cells, tumor types,etc., to facilitate the development of actionable information.

According to some aspects, the treatment and outcome informationprovided can be of limited value unless the information facilitatestreatment decisions, without unduly impacting the amount of time theuser (e.g., physician) spends to utilize that information. In someembodiments, the outcome system can be configured to limit data inputfor a single patient to a matter of minutes and provide resultingsummary information responsive to any submission. In one embodiment,physicians and other users provide outcome data for particular patientsin an interface that permits simple classification of outcome data.Outcome data that is normalized from multiple sources (e.g., patientdata, references, trials, etc.) may be presented to the physician andmay lead to more effective treatments.

According to one embodiment, the outcome system can be configured toaggregate collected outcome data and associated therapy information intoa central database. Other sources of outcome data (e.g., formal registrystudies and outcome data from academic medical center partnerships) canbe combined with a central database to create a large and rich outcomedata source that can be accessed by users of an outcome system.According to one embodiment, a global data model for cancer treatmentoutcomes can enable the integration of the variety of data sources intoa consistent and easily navigated information source. For example, thecentral database organized under the global model can be used to providethe cancer treatment outcome information according to specificvisualizations presented to end users. In various embodiments, theoutcome system is configured to provide functions as a mechanism togather outcome data and to visualize the outcome data. This contrastswith conventional approaches that do not aggregate various sources ofinformation, and do not distill the information into an actionable formbased on, for example, a patient's analyzed tumor.

According to another aspect, it is realized that physicians and othermedical personnel would benefit by having a tool that would allow themto locate more quickly appropriate treatment and outcome information.Further, adoption and use of, for example, the outcome system can bedirectly impacted by how much time it takes to provide informationand/or view valuable information in return. According to variousembodiments, the outcome system can be specially configured to minimizethe time to input useful information. For example, the system can beconfigured to categorize complex treatments and outcomes into intuitiveand visually selectable categories. The categorizations andvisualizations enable quick and easy entry of sophisticated andvoluminous data, while preserving the value represented by the inputtreatment and outcome information.

Some embodiments relate to an outcome system that is capable ofgenerating in real-time treatment and outcome time line displays, as itis appreciated that treatment is a process and can be analyzed as afunction of time. For example, time line displays may be provided thatsummarize treatment and display any associated outcome of the treatmentfor each patient over time. In some embodiments, input treatment andoutcome information can also be used to provide information associatedwith similar patients having similar timeline information. For example,the outcome system can identify similar patients based on matchingpatient condition and treatment information (including e.g., genomicalteration test results, tumor type, affected gene, treatment, etc.)over time. The outcome system can identify those similar patients anddisplay their information such that valuable treatment and outcomeinformation for other patients can be easily navigated to obtainrelevant and related treatment/outcome information.

According to one example, the outcome system can provide for selectionsin a user interface to navigate to information on system identifiedsimilar patients. Further, navigation options can be generated to directthe user to valuable information contained in public information sources(e.g., clinicaltrials.gov). In other embodiments, proprietaryinformation sources can also be accessed via system generated navigationlinks to provide such similar patient information and genomic testinginformation.

According to one aspect, a system for tracking and analysis of cancertreatment and outcome information is provided. The system comprises atleast one processor operatively connected to a memory, the at least oneprocessor when executing is configured to receive treatment and outcomeinformation associated with a patient from at least one user, organizethe treatment and the outcome information according to one or more ofalteration, affected gene, affected pathway, tumor type, and treatment,generate outcome summary information including course of treatmentdisplays over time, and communicate the outcome summary information tothe at least one user.

In one embodiment, the treatment information includes any one or more ofdrugs, therapeutics, named drugs, named therapeutics, drug cocktails,drug combinations, radiation, and surgery. In one embodiment, theoutcome information includes information regarding a status of apatient's cancer. In one embodiment, the status of the patient's cancerincludes one or more of complete response, partial response, stabledisease, and progressive disease. In one embodiment, the course oftreatment includes information regarding how patient is responding totreatment over time.

In one embodiment, the system further comprises an analysis componentexecuted by the at least one processor configured to identify similarpatients based on information related to genomic alteration. In oneembodiment, the system further comprises an analysis component executedby the at least one processor configured to identify similar patientsbased on information related to affected gene identified in a cancer. Inone embodiment, the system further comprises an analysis componentexecuted by the at least one processor configured to identify similarpatients based on information related to treatment. In one embodiment,the system further comprises an analysis component executed by the atleast one processor configured to identify similar patients based onrelated to tumor type. In one embodiment, the system further comprisesan analysis component executed by the at least one processor configuredto identify similar patients based on information relating to acombination of at least two or more of a group comprising alteration,affected gene, affected pathway, tumor type, and treatment.

In one embodiment, the system further comprises an analysis componentexecuted by the at least one processor configured to identify similarpatients based on information related to at least one of alteration,affected gene, affected pathway, tumor type, and treatment for apatient's cancer, wherein the analysis component is configured toaggregate responsive information according to one or more of alteration,affected gene, affected pathway, tumor type, and treatment. In oneembodiment, the analysis component is configured to aggregate similarpatients within classes of alterations. In one embodiment, the classesof alteration include alterations in a specified domain of a gene. Inone embodiment, the domain includes at least a kinase domain of thegene.

In one embodiment, the gene includes BRAF, and the specific domainsinclude at least one of kinase, BRAF V600E, and BRAF V600K. In oneembodiment, analysis component can aggregate alteration on all BRAF V600mutations together or all of the mutations in the kinase domain of BRAF.In one embodiment, the analysis component is configured to aggregatealteration information according to pathways affected by respectivealterations. In one embodiment, the analysis component is configured toaggregate similar patient information based on functional similarity ofidentified alterations, which can be determined for distinct mutationshaving functionally similar characteristics in the cancer cells.

In one embodiment, the system further comprises a reminder componentexecuted by the at least one processor configured to communicate anupdate request to the at least one user. In one embodiment, the remindercomponent is configured to determine a scheduled period for a patientupdate has expired. In one embodiment, the reminder component isconfigured to communicate an estimated time to complete the updaterequest.

In one embodiment, the system further comprises an input componentexecuted by the at least one processor configured to determine a type ofinformation required for a patient. In one embodiment, the inputcomponent is configured to determine the type of information required isone of treatment and outcome information based on analysis of a patientrecord. In one embodiment, the input component is configured to generatean update request according to the type of information required. In oneembodiment, the input component is configured to analyze the patientrecord to determine if treatment information has been input. In oneembodiment, the input component is configured to determine an estimatedtime to input information based on the update request and the type ofinformation.

In one embodiment, the system further comprises an analysis componentexecuted by the at least one processor configured to compare a currentpatient record to existing treatment information. In one embodiment, theexisting treatment information includes at least one of alteration,affected gene, affected pathway, tumor type, and one or more treatments.In one embodiment, the analysis component is configured to identifysimilar patients based on information in the current patient record,wherein identifying the similar patients includes determining a matchbetween the current patient record and at least one of alteration,affected gene, affected pathway, tumor type, and treatment. In oneembodiment, the analysis component is configured to identify similarpatients based on user selection of at least one of tumor type,alteration, gene, and treatment. In one embodiment, the analysiscomponent is configured to filter a grouping of similar patients basedon additional specification of at least one of alteration, affectedgene, affected pathway, tumor type, and treatment.

In one embodiment, the system further comprises a connection componentexecuted by the at least one processor configured to provide connectioninformation associated with care providers for respective patientswithin a group of similar patients. In one embodiment, the connectioncomponent is configured to provide contact information based on userselection of permission options.

In one embodiment, the system further comprises a UI component executedby the at least one processor configured to display treatment andoutcome information for a patient within a history timeline. In oneembodiment, the UI component is configured to enable navigation withintreatment and outcome information based on selection of alteration,affected gene, affected pathway, tumor type, and treatment. In oneembodiment, the UI component is configured to present selection elementsfor one of more of alteration, affected gene, affected pathway, tumortype, and treatment. In one embodiment, the selection elements areconfigured to cause the system to identify a subset of matching patientrecords according to specification of one or matching criteria with theselection elements.

In one embodiment, the UI component is configured to present a generaltreatment display configured to group a plurality of matching patientsaccording to a common treatment. In one embodiment, the UI component isconfigured to present a similar patient view of a plurality of matchingpatients, wherein the similar patient view is configured to displaygroupings of patient records matching information in a current patientrecord. In one embodiment, the UI component is configured to determinethe matching information based on one or more of alteration, affectedgene, affected pathway, tumor type, and treatment. In one embodiment,the UI component is further configured to display filter options withinthe selection elements based on one or more of the alteration, affectedgene, affected pathway, tumor type, and treatment information for thecurrent patient record.

In one embodiment, the UI component is configured to transition from thesimilar patient view to a detailed view of outcome information for agroup of patients based on selection of filter data presented in thesimilar patient view. In one embodiment, selection of the filter dataincludes specification of filter data for alteration, affected gene,affected pathway, tumor type, and treatment associated with a pluralityof patients' cancers. In one embodiment, the detailed view of theoutcome information is configured to display a respective outcome foreach respective patient within the group of patients. In one embodiment,the UI component is configured to transition to a view of the respectivepatient's information based on selection of the respective patientdisplay in the detailed view of the outcome information.

In one embodiment, the UI component is configured to acceptspecification of filter data for one or more of alteration, affectedgene, affected pathway, tumor type, and treatment associated with aplurality of patients to display treatment and outcome information. Inone embodiment, the UI component is configured to display a detailedview of treatment and outcome information for a patient population basedon specifying filter data for alteration, affected gene, affectedpathway, tumor type, and treatment.

In one embodiment, the system further comprises a storage componentexecuted by the at least one processor configured to manage cancertreatment and outcome information according to a data model. In oneembodiment, the data model comprises a data structure associated withpatient records, and wherein the data structure includes data recordsfor specification of alteration, affected gene, affected pathway, tumortype, and treatment.

According to one aspect, a computer implemented method for tracking andanalysis of cancer treatment and outcome information is provided. Themethod comprises receiving, by a computer system, treatment and outcomeinformation associated with a patient from at least one user,organizing, by the computer system, the treatment and the outcomeinformation according to one or more of alteration, affected gene,affected pathway, tumor type, and treatment, generating, by the computersystem, outcome summary information including course of treatmentdisplays over time, and communicating, by the computer system, theoutcome summary information to the at least one user.

According to one embodiment, the treatment information includes any oneor more of drugs, therapeutics, named drugs, named therapeutics, drugcocktails, drug combinations, radiation, and surgery. According to oneembodiment, the outcome information includes information regarding astatus of a patient's cancer. According to one embodiment, the status ofthe patient's cancer includes one or more of complete response, partialresponse, stable disease, and progressive disease. According to oneembodiment, the course of treatment includes information regarding howpatient is responding to treatment.

According to one embodiment, the method further comprises identifying,by the computer system, similar patients based on information related togenomic alteration. According to one embodiment, the method furthercomprises identifying, by the computer system, similar patients based oninformation related to affected gene identified in a cancer. Accordingto one embodiment, the method further comprises identifying, by thecomputer system, similar patients based on information related totreatment. According to one embodiment, the method further comprisesidentifying, by the computer system, similar patients based on relatedto tumor type. According to one embodiment, the method further comprisesidentifying, by the computer system, similar patients based oninformation relating to a combination of at least two or more of a groupcomprising alteration, affected gene, affected pathway, tumor type, andtreatment. According to one embodiment, the method further comprisesidentifying, by the computer system, similar patients based oninformation related to at least one of alteration, affected gene,affected pathway, tumor type, and treatment for a patient's cancer, andaggregating, by the computer system, responsive information according toone or more of alteration, affected gene, affected pathway, tumor type,and treatment.

According to one embodiment, the method further comprises aggregating,by the computer system, similar patients within classes of alterations.According to one embodiment, the classes of alteration includealterations in a specified domain of a gene. According to oneembodiment, the domain includes at least a kinase domain of the gene.

According to one embodiment, the gene includes BRAF, and the specificdomains include at least one of kinase, BRAF V600E, and BRAF V600K.According to one embodiment, the method further comprises aggregating,by the computer system, alteration information according to pathwaysaffected by respective alterations. According to one embodiment, themethod further comprises aggregating, by the computer system, similarpatient information based on functional similarity of identifiedalterations, which can be determined for distinct mutations havingfunctionally similar characteristics in the cancer cells.

According to one embodiment, the method further comprises communicating,by the computer system, an update request to the at least one user.According to one embodiment, the method further comprises determining,by the computer system, a scheduled period for a patient update hasexpired. According to one embodiment, communicating the update requestincludes communicating an estimated time to complete the update request.According to one embodiment, the method further comprises determining,by the computer system, a type of information required for a patient.According to one embodiment, the method further comprises determining,by the computer system, the type of information required is one oftreatment and outcome information based on analysis of a patient record.According to one embodiment, the method further comprises generating, bythe computer system, an update request according to the type ofinformation required.

According to one embodiment, the method further comprises analyzing, bythe computer system, the patient record to determine if treatmentinformation has been input. According to one embodiment, the methodfurther comprises determining, by the computer system, an estimated timeto input information based on the update request and the type ofinformation. According to one embodiment, the method further comprisescomparing, by the computer system, a current patient record to existingtreatment information. According to one embodiment, the existingtreatment information includes at least one of alteration, affectedgene, affected pathway, tumor type, and one or more treatments.

According to one embodiment, the method further comprises identifying,by the computer system, similar patients based on information in thecurrent patient record, wherein identifying the similar patientsincludes determining a match between the current patient record and atleast one of alteration, affected gene, affected pathway, tumor type,and treatment. According to one embodiment, the method further comprisesidentifying, by the computer system, similar patients based on userselection of at least one of tumor type, alteration, genes, andtreatment. According to one embodiment, the method further comprisesfiltering, by the computer system, a grouping of similar patients basedon additional specification of at least one of alteration, affectedgene, affected pathway, tumor type, and treatment. According to oneembodiment, the method further comprises providing, by the computersystem, connection information associated with care providers forrespective patients within a group of similar patients.

According to one embodiment, the method further comprises providing, bythe computer system, contact information based on user selection ofpermission options. According to one embodiment, the method furthercomprises displaying, by the computer system, treatment and outcomeinformation for a patient within a history timeline. According to oneembodiment, the method further comprises navigating, by the computersystem, within treatment and outcome information display in a userinterface based on selection of alteration, affected gene, affectedpathway, tumor type, and treatment. According to one embodiment, themethod further comprises displaying, by the computer system, selectionelements for one of more of alteration, affected gene, affected pathway,tumor type, and treatment. According to one embodiment, the selectionelements are configured to cause the system to identify a subset ofmatching patient records according to specification of one or matchingcriteria with the selection elements. According to one embodiment, themethod further comprises displaying, by the computer system, a generaltreatment display configured to group a plurality of matching patientsaccording to a common treatment.

According to one embodiment, the method further comprises displaying, bythe computer system, a similar patient view of a plurality of matchingpatients, wherein the similar patient view is configured to displaygroupings of patient records matching information in a current patientrecord. According to one embodiment, the method further comprisesdetermining, by the computer system, the matching information based onone or more of an alteration, affected gene, affected pathway, tumortype, and treatment. According to one embodiment, the method furthercomprises displaying, by the computer system, filter options within theselection elements based on one or more of the alteration, affectedgene, affected pathway, tumor type, and treatment information for thecurrent patient record.

According to one embodiment, the method further comprises transitioning,by the computer system, from the similar patient view in a userinterface to a detailed view of outcome information for a group ofpatients based on selection of filter data presented in the similarpatient view. According to one embodiment, selection of the filter dataincludes specification of filter data for alteration, affected gene,affected pathway, tumor type, and treatment associated with a pluralityof patients' cancers. According to one embodiment, the detailed view ofthe outcome information is configured to display a respective outcomefor each respective patient within the group of patients. According toone embodiment, the method further comprises comprising transitioning,by the computer system, to a view of the respective patient'sinformation based on selection of the respective patient display in thedetailed view of the outcome information.

According to one embodiment, the method further comprises accepting, bythe computer system, specification of filter data for one or more ofalteration, affected gene, affected pathway, tumor type, and treatmentassociated with a plurality of patients to display treatment and outcomeinformation. According to one embodiment, the method further comprisesdisplaying, by the computer system, a detailed view of treatment andoutcome information for a patient population based on specifying filterdata for alteration, affected gene, affected pathway, tumor type, andtreatment. According to one embodiment, the method further comprisesmanaging, by the computer system, cancer treatment and outcomeinformation according to a data model. According to one embodiment, thedata model comprises a data structure associated with patient records,and wherein the data structure includes data records for specificationof alteration, affected gene, affected pathway, tumor type, andtreatment.

According to one aspect, a computer-readable medium havingcomputer-readable signals stored thereon that define instructions that,as a result of being executed by a computer, instruct the computer toperform a method for tracking and analysis of cancer treatment andoutcome information is provided. The method comprises receivingtreatment and outcome information associated with a patient from atleast one user, organizing the treatment and the outcome informationaccording to one or more of alteration, affected gene, affected pathway,tumor type, and treatment, generating outcome summary informationincluding course of treatment displays over time, and communicating theoutcome summary information to the at least one user.

According to one embodiment, the treatment information includes any oneor more of drugs, therapeutics, named drugs, named therapeutics, drugcocktails, drug combinations, radiation, and surgery. According to oneembodiment, the outcome information includes information regarding astatus of a patient's cancer. According to one embodiment, the status ofthe patient's cancer includes one or more of complete response, partialresponse, stable disease, and progressive disease. According to oneembodiment, the course of treatment includes information regarding howpatient is responding to treatment.

According to one embodiment, the method further comprises identifyingsimilar patients based on information related to genomic alteration.According to one embodiment, the method further comprises identifyingsimilar patients based on information related to affected geneidentified in a cancer. According to one embodiment, the method furthercomprises identifying similar patients based on information related totreatment. According to one embodiment, the method further comprisesidentifying similar patients based on related to tumor type. Accordingto one embodiment, the method further comprises identifying similarpatients based on information relating to a combination of at least twoor more of a group comprising alteration, affected gene, affectedpathway, tumor type, and treatment. According to one embodiment, themethod further comprises identifying similar patients based oninformation related to at least one of alteration, affected gene,affected pathway, tumor type, and treatment for a patient's cancer, andaggregating responsive information according to one or more ofalteration, affected gene, affected pathway, tumor type, and treatment.

According to one embodiment, the method further comprises aggregatingsimilar patients within classes of alterations. According to oneembodiment, the classes of alteration include alterations in a specifieddomain of a gene. According to one embodiment, the domain includes atleast a kinase domain of the gene. According to one embodiment, the geneincludes BRAF, and the specific domains include at least one of kinase,BRAF V600E, and BRAF V600K. According to one embodiment, the methodfurther comprises aggregating alteration information according topathways affected by respective alterations. According to oneembodiment, the method further comprises aggregating similar patientinformation based on functional similarity of identified alterations,which can be determined for distinct mutations having functionallysimilar characteristics in the cancer cells.

According to one embodiment, the method further comprises communicatingan update request to the at least one user. According to one embodiment,the method further comprises determining a scheduled period for apatient update has expired. According to one embodiment, communicatingthe update request includes communicating an estimated time to completethe update request. According to one embodiment, the method furthercomprises determining a type of information required for a patient.According to one embodiment, the method further comprises determiningthe type of information required is one of treatment and outcomeinformation based on analysis of a patient record. According to oneembodiment, the method further comprises generating an update requestaccording to the type of information required.

According to one embodiment, the method further comprises analyzing thepatient record to determine if treatment information has been input.According to one embodiment, the method further comprises determining anestimated time to input information based on the update request and thetype of information. According to one embodiment, the method furthercomprises comparing a current patient record to existing treatmentinformation. According to one embodiment, the existing treatmentinformation includes at least one of alteration, affected gene, affectedpathway, tumor type, and one or more treatments.

According to one embodiment, the method further comprises identifyingsimilar patients based on information in the current patient record,wherein identifying the similar patients includes determining a matchbetween the current patient record and at least one of alteration,affected gene, affected pathway, tumor type, and treatment. According toone embodiment, the method further comprises identifying similarpatients based on user selection of at least one of tumor type,alteration, genes, and treatment. According to one embodiment, themethod further comprises filtering a grouping of similar patients basedon additional specification of at least one of alteration, affectedgene, affected pathway, tumor type, and treatment. According to oneembodiment, the method further comprises providing connectioninformation associated with care providers for respective patientswithin a group of similar patients.

According to one embodiment, the method further comprises providingcontact information based on user selection of permission options.

According to one embodiment, the method further comprises displayingtreatment and outcome information for a patient within a historytimeline. According to one embodiment, the method further comprisesnavigating within treatment and outcome information display in a userinterface based on selection of alteration, affected gene, affectedpathway, tumor type, and treatment. According to one embodiment, themethod further comprises displaying selection elements for one of moreof alteration, affected gene, affected pathway, tumor type, andtreatment. According to one embodiment, the selection elements areconfigured to cause the system to identify a subset of matching patientrecords according to specification of one or matching criteria with theselection elements. According to one embodiment, the method furthercomprises displaying a general treatment display configured to group aplurality of matching patients according to a common treatment.

According to one embodiment, the method further comprises displaying asimilar patient view of a plurality of matching patients, wherein thesimilar patient view is configured to display groupings of patientrecords matching information in a current patient record. According toone embodiment, the method further comprises determining the matchinginformation based on one or more of an alteration, affected gene,affected pathway, tumor type, and treatment. According to oneembodiment, the method further comprises displaying filter optionswithin the selection elements based on one or more of the alteration,affected gene, affected pathway, tumor type, and treatment informationfor the current patient record.

According to one embodiment, the method further comprises transitioningfrom the similar patient view in a user interface to a detailed view ofoutcome information for a group of patients based on selection of filterdata presented in the similar patient view. According to one embodiment,selection of the filter data includes specification of filter data foralteration, affected gene, affected pathway, tumor type, and treatmentassociated with a plurality of patients' cancers. According to oneembodiment, the detailed view of the outcome information is configuredto display a respective outcome for each respective patient within thegroup of patients. According to one embodiment, the method furthercomprises comprising transitioning to a view of the respective patient'sinformation based on selection of the respective patient display in thedetailed view of the outcome information.

According to one embodiment, the method further comprises acceptingspecification of filter data for one or more of alteration, affectedgene, affected pathway, tumor type, and treatment associated with aplurality of patients to display treatment and outcome information.According to one embodiment, the method further comprises displaying adetailed view of treatment and outcome information for a patientpopulation based on specifying filter data for alteration, affectedgene, affected pathway, tumor type, and treatment. According to oneembodiment, the method further comprises managing cancer treatment andoutcome information according to a data model. According to oneembodiment, the data model comprises a data structure associated withpatient records, and wherein the data structure includes data recordsfor specification of alteration, affected gene, affected pathway, tumortype, and treatment.

Still other aspects, embodiments, and advantages of these exemplaryaspects and embodiments, are discussed in detail below. Any embodimentdisclosed herein may be combined with any other embodiment in any mannerconsistent with at least one of the objects, aims, and needs disclosedherein, and references to “an embodiment,” “some embodiments,” “analternate embodiment,” “various embodiments,” “one embodiment” or thelike are not necessarily mutually exclusive and are intended to indicatethat a particular feature, structure, or characteristic described inconnection with the embodiment may be included in at least oneembodiment. The appearances of such terms herein are not necessarily allreferring to the same embodiment. The accompanying drawings are includedto provide illustration and a further understanding of the variousaspects and embodiments, and are incorporated in and constitute a partof this specification. The drawings, together with the remainder of thespecification, serve to explain principles and operations of thedescribed and claimed aspects and embodiments.

BRIEF DESCRIPTION OF THE DRAWINGS

Various aspects of at least one embodiment are discussed below withreference to the accompanying figures, which are not intended to bedrawn to scale. Where technical features in the figures, detaileddescription or any claim are followed by reference signs, the referencesigns have been included for the sole purpose of increasing theintelligibility of the figures, detailed description, and claims.Accordingly, neither the reference signs nor their absence, are intendedto have any limiting effect on the scope of any claim elements. In thefigures, each identical or nearly identical component that isillustrated in various figures is represented by a like numeral. Forpurposes of clarity, not every component may be labeled in every figure.The figures are provided for the purposes of illustration andexplanation and are not intended as a definition of the limits of theinvention. In the figures:

FIG. 1 is a diagram of a system for managing genomic testing informationusing an alteration engine, according to one embodiment;

FIG. 2 is a diagram of a system for managing genomic testinginformation, according to one embodiment;

FIG. 3 is an example process flow for a method of managing genomictesting information, according to one embodiment;

FIG. 4 is an example process flow for a method of navigating genomictesting information, according to one embodiment;

FIG. 5 is a block diagram of one example of a computer system that maybe used to perform processes and functions disclosed herein.

FIG. 6 is an example user interface, according to one embodiment;

FIGS. 7A-K are example user interface screen captures, according to oneembodiment;

FIGS. 8A and 8E are example user interface screen captures, according toone embodiment;

FIGS. 8B-D are example user interface screen captures, according to oneembodiment;

FIGS. 9A and 9O illustrate an example of a static genomic alterationreport, according to one embodiment;

FIGS. 9B-9N illustrate an example of a static genomic alteration report,according to one embodiment;

FIG. 10 is a diagram of a system for capturing and processing treatmentand outcome information using an outcome engine;

FIG. 11 is a diagram of a system for capturing and processing treatmentand outcome information;

FIG. 12 is an example process flow for a method of capturing andprocessing treatment and outcome information, according to oneembodiment;

FIG. 13 is an example process flow for a method of navigating treatmentand outcome information, according to one embodiment;

FIG. 14 is a block diagram of one example of a computer system that maybe used to perform processes and functions disclosed herein;

FIG. 15 is a screen capture of an update request message, according toone embodiment;

FIG. 16 is a screen capture of an electronic message, according to oneembodiment;

FIG. 17 is an example account login page, according to one embodiment;

FIG. 18 is an example user interface, according to one embodiment;

FIG. 19 is an example user interface, according to one embodiment;

FIG. 20 is an example user interface, according to one embodiment;

FIG. 21 is an example user interface, according to one embodiment;

FIG. 22 is an example user interface, according to one embodiment;

FIG. 23 is an example user interface, according to one embodiment;

FIG. 24 is a user selection within an example user interface totransition to a next patient from a timeline display, according to oneembodiment;

FIG. 25 is an example user interface, according to one embodiment;

FIG. 26 is an example user interface, according to one embodiment;

FIG. 27 is an example user interface displaying additional detail,according to one embodiment;

FIG. 28 is an example user interface, according to one embodiment;

FIG. 29 is a screen capture of an example interface including displaysfor similar patients, according to one embodiment;

FIG. 30A-B show an example user interface including drop-down menus forspecifying filter criteria on a patient population, according to oneembodiment;

FIG. 31 is an example user interface showing a detailed view of patientoutcomes within a patient group;

FIG. 32A-B illustrate an example site map, according to one embodiment;

FIG. 33 illustrates an example trial summary page, according to oneembodiment;

FIG. 34 illustrates an example reference summary view, according to oneembodiment;

FIG. 35 illustrates an example user interface for defining system alertpreferences, according to one embodiment;

FIG. 36 illustrates an example user interface for defining alerts,according to one embodiment;

FIG. 37 illustrates an example general framework design for a genomicuser interface, according to one embodiment;

FIG. 38A-D illustrate example content items, according to oneembodiment;

FIG. 39 illustrates an example page accessible via as part of a genomicreport, according to one embodiment;

FIG. 40A-C illustrate information in example views shown in anunexpanded or collapsed state, according to one embodiment;

FIG. 41A-B illustrate information in example views shown in an expandedstate, according to one embodiment;

FIG. 42 illustrates example update indicators, according to oneembodiment;

FIG. 43 illustrates example alert indicators, according to oneembodiment;

FIG. 44 illustrates another embodiment of a test report view;

FIG. 45 illustrates an example test report view including information ina collapsed state;

FIG. 46A-B illustrate an example test report view including informationin an expanded state;

FIG. 47A-B illustrate an example execution flow between respective pagesof a genomic testing website, according to one embodiment;

FIG. 48 illustrates an example flow for configuration of systembehavior, according to one embodiment;

FIG. 49 illustrates an example flow for accessing aggregated genomictesting information in a community portal;

FIG. 50A-C illustrate an example knowledge base page, according to oneembodiment;

FIG. 51A-C illustrate an example trial index page, according to oneembodiment;

FIG. 52A-C illustrates an example patient case study, according to oneembodiment; and

FIG. 53A-C shows an example user profile page, according to oneembodiment.

DETAILED DESCRIPTION

As described above, conventional knowledge bases (e.g.,ClinicalTrials.gov) are insufficient to capture large portions oftreatment and outcome information from physicians and their patients.Further, conventional aggregations of treatment and outcome informationfail to provide actionable and/or usable data in a manner that wouldallow a physician to assimilate that information into their dailypractice and treatment decision making in a timely manner.

According to one embodiment, an outcome system is provided that includesan outcome engine configured to generate requests for physicians toprovide treatment and outcome information specific to their patients.The outcome engine generates a user interface presented to the physicianfor inputting treatment and outcome information such that the timerequired for a physician to input data is minimized (e.g., usingintuitive user interfaces). In one embodiment, the outcome engine isconfigured to categorize complex treatment and outcome information intosimple visual selections that convey valuable information to physiciansfor use in treatment decision-making. According to another embodiment,treatment and outcome information is focused on cancer therapies and canbe organized based on genomic alteration, tumor type, and therapy beingapplied. Various embodiments can facilitate user entry and display ofpatient outcome information within the organizations of genomicalteration, tumor type, and therapy.

Further embodiments can incorporate genomic testing information on apatient's cancer to develop actionable information. In one example,testing performed on patient cancer tissue can be included as part of apatient. In further examples, information on the tumor type, genomicalterations found, candidate treatment options, etc., can be used tomatch a current patient to other treatment and outcome information onthe system.

Responsive to treatment and outcome information input, the outcomeengine can be configured to generate outcome information for one or morepatients carrying a particular genomic alteration, carrying alterationsto genes implicated in a particular pathway, having a particular tumortype, or having received a particular therapy, as a function of time(e.g., within a timeline display). In one embodiment, such interfacescan be presented immediately in response to user input. According tosome embodiments, the timeline displays visually summarize course oftreatment data from patients sharing given characteristics in anintuitive format configured to provide actionable or advisoryinformation for treatment decision making. In one embodiment, outcomedata is normalized in one or more categories that may be easilyinterpreted by a physician or other user.

In some embodiments, the outcome engine facilitates data navigation bythe user. For example, the outcome engine can identify and providenavigation options to information on similar patients (e.g., usinggenomic alteration, treatment, and/or tumor information to match relatedand/or similar information). The patient information can be correlatedby the engine within treatment and outcomes to enable the system toconvey valuable information on populations of similar patients, theirtreatments, and their outcomes.

Referring to FIG. 10, there is illustrated one example of a system 1000for processing treatment and outcome information using an outcome engine1004. Elements of the system 1000 can be provided using a computingsystem such as the computer system 1400 and/or 1402 described withreference to FIG. 14. For example, the outcome engine 1004 can beexecuted on the computer system 1400 and/or 1402 to provide thefunctions and operations discussed herein. In other embodiments, theoutcome engine 1004 can include additional components executed on thecomputer system to perform specific operations.

As shown in FIG. 10, various embodiments of the outcome engine 1004 areconfigured to receive input from a remote system operated by a user. Forexample, the user can access the system 1000 to input treatment andoutcome information 1002 (e.g., treatment and outcome informationspecific to the user's patients). Responsive to entry of the treatmentand outcome information 1002, the outcome engine 1004 can be configuredto generate and display diagnostic information to the user at 1006. Forexample, treatment and outcome information can be displayed based onquery criteria (e.g., alteration, affected gene or pathway, tumor type,treatment) as an information display 1006, as soon as the treatment andoutcome information is saved on system 1000. In some examples, theinformation display 1006 is designed to facilitate treatment for a givenpatient by providing treatment and outcome information for patients withsimilar characteristics (e.g., genomic alterations, alterations to givengene(s) or pathway(s), tumor types, etc.). In one embodiment, patientshaving similar characteristics can also be identified based onalterations in a level of expression of a gene and/or associatedprotein. In one example, testing can identify alterations in expressionthrough analysis of suitable vectors for determining expression. Variousembodiments are configured to enable a user to review anycharacteristics available (e.g., genomic alterations, alterations togiven gene(s) or pathway(s), tumor types, expression level, etc.) tofacilitate treatment.

For example, the information display 1006 is generated such that theuser (e.g., a physician) can understand and interpret the informationreadily from the display (e.g., see patient history timelines shown inFIG. 23, FIG. 24 and FIG. 26). In a cancer treatment setting, variousones of the displays can be organized based on a tumor type identifiedfor the patient and a genomic alteration associated with the patient(e.g., see FIG. 30 and FIG. 31 discussed in greater detail below).Additional information regarding treatment can also be provided whereavailable.

According to one embodiment, the outcome engine 1004 facilitatescollection and analysis of the treatment and outcome information bysimplifying the input of sophisticated and extensive treatment andoutcome information. For example, the outcome engine 1004 can include aninput component 1100 configured to organize data being entered intotumor type (if not already known), genomic alteration (if not alreadyknown), and treatment options. In some embodiments, an affected gene orgenes can also be specified in the patient record. The input componentcan be configured to allow the user to enter specific information withinany of the preceding options and narrow the data entry based on anyknown information (e.g., genomic alteration, affected gene or pathway,tumor type, expression etc.). Once input, the combined information canbe used by the system 1000 and/or outcome engine 1004 to provideinformation on outcomes associated with patients within any one or moretumor type, genomic alteration, and treatment.

Further, the input component 1010 can be configured to present treatmentinformation based on system categorizations. In the cancer treatmentsetting, the outcome engine 1004 accepts treatment information bypresenting treatment categories defined by the input component 1010 forselection by the user. In one example, a user interface can be generatedby the system 1000 and displayed on a respective computer system of theuser (e.g., example user interface displays are shown in FIGS. 15-31).Further, the outcome engine 1004 can include a user interface (“UI”)component 1012 configured to generate user interfaces displayed by thesystem. The UI component 1012 accesses categories defined on the system,for example, by the input component 1010 and generate user interfacedisplays to accept input treatment and/or outcome informationaccordingly.

In the cancer treatment example, the displayed categories for treatmentcan include therapeutic agent or regimen, radiation, and/or surgery,among other options. As discussed, the organization on tumor type,alteration, and therapy facilitates ease and speed of data access. Forexample, using categorizations of therapy and outcome information,within one or two clicks of a mouse, cancer treatment information can besubmitted to the system for a specific patient (e.g., surgery—2 clicks(click “add treatment,” click “surgery,” radiation—2 clicks, click “addtreatment,” click “radiation” as shown in FIG. 19). Example userinterface displays are shown in FIG. 15-31, which include displays andfunctionality for entering treatment information. In further examples,the system 1000 can be configured to default to adding treatmentinformation upon accessing a patient record without treatment datareducing the number of clicks for selecting a treatment (e.g., surgeryor radiation) to 1 click each.

FIG. 18 shows a user interface 1800 for inputting treatment information.At 1804, a currently selected patient's information is displayed. At1802, a user can navigate between displayed patients including patientslisted at 1802A-C. At 1806, a recently updated menu can be displayed toprovide access to recently updated patient information (e.g., at1806A-F). For the currently selected patient “Erik Fairbairn,” the userprovided options to add treatment information associated with thecurrent patient, for example, at 1808. In one embodiment, treatmentinformation can be added by selecting a drop down menu 1808. Oncetreatment information has been defined, the input information can besaved, by selecting 1810. If the user does not wish to add treatmentinformation, the user can select “skip for now” at 1812.

In one embodiment, the patient treatment user interface 1800 can provideaccess to any genomic testing reports associated with the selectedpatient. For example, the user can select display 1814 to access genomicreports for the patient (discussed in greater detail herein).Additionally, similar patients can also be accessed through displays onpage 1800, at 1816. For example, the system can identify similarpatients based on matches between any one or more of: genomicalterations, affected genes or pathways, treatments, and/or tumor types.The system identified similar patients can then be accessed by selectingdisplay 1816. In some embodiments, the system can be configured todynamically identify similar patients to a current patient record. Inone example, responsive to entry of new treatment information, systemdetermined similar patients can be updated. For example, if newtreatment information is entered at 1808, display 1816 can changeaccording to new matches against, for example, specified treatmentinformation.

FIG. 19 is an example user interface 1900. Interface 1900 includes adrop down menu at 1902 for selecting from types of treatment for apatient. At 1902, a user has selected “Add treatment,” and the user mayselect from pre-defined options at 1904—therapeutic agent or regimen,1906—radiation, and 1908—surgery. Once a particular treatment option hasbeen entered, that treatment can be saved by the system.

For therapeutic agent or regimen as a treatment option, the outcomeengine 1004 and/or input component 1010 can also be configured to accepttext input to specify a particular agent or regimen (e.g., as shown inFIGS. 20 at 2002 and FIG. 21 at 2102). In some embodiments, the outcomeengine 1004 can be configured to present a search interface foridentifying a therapeutic agent or regimen. Optionally, the outcomeengine provides a user interface element through the UI component 1012for accepting search criteria.

FIG. 20 illustrates an example user interface 2000. Interface 2000displays options for entering specific treatment information at 2002.Responsive to selecting therapeutic agent or regimen (e.g., at 1904 ofFIG. 19), the user interface can display a text input box at 2002. Thetext input box allows users to search agents and regimens to facilitateuser selection. At 2006, the user interface provides options forentering a start date associated with the treatment. At 2008, the userinterface can also provide options for entering additional detailregarding the treatment. For example, at 2008 the user can specify thatthe treatment information being entered is part of a clinical trial. Theclinical trial indicator can be used to match similar patients, identifyand/or link to the clinical trial, etc. Interface 2000 can also beconfigured to accept multiple treatment options. For example, selectionof 2010 enables entry of multiple treatments, and even multipletreatments of the same kind.

FIG. 21 is an example user interface 2100. Interface 2100 illustratessearch functionality provided as part of entering treatment information.At 2102, a text search box displays potential matches to the userresponsive to their input. For example, “Er” entered at 2104 is matchedby the system to candidate treatments “Erbitux” at 2106, “Erlotinib” at2108, and “Erwinia L-asparaginese” at 2110. The user can select fromdisplayed options or finish typing in treatment information.Additionally, the user may delete a treatment responsive to selecting2112 “Delete treatment.” FIG. 22 shows an example user interface wherethe user has selected or input a specific treatment (“Erbitux” at 2202).Once any treatment information is input, the user can save thatinformation. For example, treatment information can be saved responsiveto selection of 2204. According to one embodiment, the user can enter avariety of treatment information prior to saving the data entered forthat patient.

In another embodiment, the outcome engine 1004 and/or UI component 1012can also be configured to accept date information associated with agiven treatment. In some embodiments, the date information is optional,as the outcome engine 1004 is configured to use a current date absentother specification by the user. Other additional data fields can beprovided. In one example, the user can specify if a treatment is beingadministered as part of a clinical trial. The outcome engine 1004 can beconfigured to use the clinical trial flag to capture additionalinformation and/or generate navigable user interface displays to directa user to associated clinical trial information.

Once the treatment information has been defined on the system, theoutcome engine 1004 and/or UI component 1012 can be configured togenerate and display a patient history timeline (e.g., FIG. 23 at 2302,FIG. 24 at 2402, and FIG. 26 at 2602). In one embodiment, the patienthistory timeline presents treatment and outcome in a visual summarydisplay. The visual summary display can be configured based on systemdefined categories for outcomes. According to some embodiments, userscan readily appreciate a course of a patient's treatment based on thedisplayed treatment and the temporal display of that treatment's outcomeover time. Additionally, the user can readily gain insight into theeffect a change in treatment may yield in a similar situation.

FIG. 26 shows four categories describing outcome information: 2604progressive disease, 2606 stable disease, 2608 partial response, and2610 complete response are shown with respect to a period of time shownat horizontal display bar 2612. Outcome information can be displayedgraphically as vertical bars reaching the outcome category for arespective time (e.g., at 2614-2622). The categories can be configuredto simplify data capture and/or entry by a user (e.g., a physician),similar to categorization of treatments. If no outcome information isavailable or outcome information has not been input, the patient historychart is configured to display the input treatment information as astart point on a timeline display without outcome information (e.g.,2402, FIG. 24).

FIG. 23 illustrates one example of a timeline display 2300. Timelinedisplay 2300 can be organized as a horizontal time-based chart ofpatient history. If the treatment information is the only informationentered the timeline display can illustrate the new information as atreatment change at 2302. FIG. 24 shows a user selection to transitionto a next patient from a timeline display. As shown, the currentpatient's treatment information is displayed as a treatment change 2404on timeline 2402. By selecting 2404, the user can quickly transition toanother patient, for example, to add and/or update treatmentinformation.

Upon selection of next patient, user interface 2500 of FIG. 25 can bedisplayed. The next patient displayed can reflect a list of patientsidentified by the system needing updates (e.g., shown at 2502). Currenttreatment information for a selected patient can be displayed at 2503.The user can update information on that treatment at 2504. For example,the user can select any one of 2506-2512, and save that information byselecting 2514. Upon saving the treatment information, the userinterface can transition to a timeline display, for example, 2600 ofFIG. 26.

If a prior date is supplied with the input treatment information theoutcome engine 1004 can also be configured to request outcomeinformation associated with the prior treatment. For example, theoutcome engine 1004 can be configured to display the input treatmentinformation (e.g., any specific agent or regimen), and display outcomecategories or classifications (e.g., progressive disease, stabledisease, partial response, and complete response) for user selection.Optionally, the outcome engine can also accept date information that canbe associated with an input outcome. In some examples, the system and/oroutcome engine can display radio buttons associated with each outcomecategory for selection in a user interface. In further examples, userscan also select date information based system specified time periods(weekly, bi-weekly, monthly, etc.), for example, as radio buttonsdisplayed in the user interface.

In some examples, user interface displays can be responsive to selectionto provide further detail entered by the user, in summary views. Forexample, user interface 2700 of FIG. 27 can provide additional detail ona display item shown on a timeline 2702. At 2704, a treatment changeicon is shown. Responsive to selection a dialogue box may be displayedto provide additional detail associated with the point on the timelinedisplay.

According to one embodiment, outcome information is provided as anupdate to existing patient records. For example, the outcome engine 1004can include a reminder component 1008 configured to deliver a request toa physician to update a patient record by inputting treatmentinformation. The reminder component 1008 can be configured to deliverthe update request via e-mail, text, etc. In some embodiments, thereminder component can be configured to estimate a length of timerequired by the user to submit requested information. In one example,the estimated time can be specified in an update request (e.g., FIG.16).

FIG. 15 is a screen capture 1500 of an update request message 1502communicated by the outcome system. FIG. 16 is a screen capture 1600 ofan electronic message (e.g., e-mail) to a user of the outcome system.Various messaging functions can be provided by the e-mail service towhich the user subscribes. For example, conventional e-mail menus areshown at 1602. Messaging window 1604 provides access to the updaterequest sent to the user. The update request sent by the system canspecify what updates are requested “Please update 3 patients,” as wellas an invitation message regarding participation in the outcomecommunity at 1606.

In one embodiment, based on analysis of the user's account and patientinformation, the system identifies what information should be updated.For example, the system can determine that treatment information isneeded for 1 patient, and status updates needed for 2 of the user'spatients (e.g., at 1608). In some examples, the system estimates anamount of time to complete the update request (e.g., at 1610). Infurther embodiments, the system can provide information on the user'spatients, and in particular, the message can include informationregarding patient consent status relating to sharing treatment andoutcome information (e.g., at 1612). The message can also include linksto information sharing authorizations at 1614. At 1616, the user canselect a link to access the outcome system and update information. Ifthe user has not logged into the outcome system, selection of “updatenow” at 1616 can bring the user to a login window. FIG. 17 shows anexample account login page.

In some embodiments, the user can identify one or more preferred methodsof contact when registering for a user account. In other embodiments,the user can also specify an order for contact methodologies, wheresubsequent contact methods are only used if no response is received toprior update requests. The reminder component 1008 can be configured torequest updated patient information on a periodic basis, according toschedule, among other options. The update request can include links thatdirect the user to specific patient records to update on system 1000(e.g., as shown in FIGS. 15-16). For example, the update request canspecify a request for updates regarding treatment being undertaken bythe patient.

Once the user accesses a patient record to provide updated information,the outcome engine 1004 can be configured to automatically associate anytreatment input with a current date (i.e., the date and/or time theoutcome information is input into the system). Further, the system canalso be configured to associate the current date to an outcome whenentered as an update to an existing patient record.

Once treatment and/or outcome information is entered on the system, theUI component 1004 can be configured to generate and display a patienthistory timeline including any outcome information provided for thepatient (e.g., FIGS. 26-29). According to one embodiment, the patienthistory timeline displays outcome categories on a y-axis and timeinformation on the x-axis. Treatment changes (e.g., start of regimen,new regimen, change in regimen, etc.) are displayed on the timeline, forexample, as milestones. In some examples, the outcome associated witheach date can be displayed as a vertical bar reaching the point on they-axis reflective of an outcome category. In some embodiments, atreatment milestone is shown on the history timeline as a visualindicator (e.g., circle, star, flag, etc.) to illustrate the start orthe change in treatment being provided. The outcome engine 1004 can beconfigured to provide additional information on the treatment, forexample, in response to hovering pointer on the visual indicator or byclicking on the visual indicator. FIG. 28 shows an example userinterface 2800 having an example indicator 2802. Responsive to selectionof “Next patient” at 2804, a user may navigate to further timelinedisplays associated with different patients.

According to another aspect, the outcome engine 1004 can also beconfigured to integrate with genomic testing services to facilitatecancer diagnosis and treatment. In one setting, a physician can requesta genomic test for a patient to determine any genomic alteration thatexists in the patient's cancer cells. The information obtained from thegenomic testing service can be used to define patient records accessibleby the outcome engine 1004. Alternatively, the outcome engine canprovide a platform on which to request genomic testing services for apatient. In some embodiments, the outcome engine 1004 can acceptelectronic or paper based genomic testing information, and associate anysuch testing information with a patient record. In one embodiment, theoutcome engine 1004 can process genomic test information to define apatient record and associate the patient record with the genomic testresults.

For users overseeing treatment of large numbers of patients, the outcomeengine 1004 can be configured to provide a display of the patientsassociated with the user as options selectable in a user interface. Inone example, a list of patients is displayed vertically along the leftedge of a display screen (e.g., FIG. 18 at 1802). Each display of apatient name is selectable to navigate to additional information on thepatient (e.g., at 1802A-C). Once a patient is selected for review, theoutcome engine 1004 displays any history information for that patient asa patient history timeline in a portion of the user interface display.The user interface display can include a visual indicator associatedwith any genomic test results for that patient. The test resultindicator can be selected in the user interface to provide additionaldetail on genomic test results.

In further embodiments, the outcome engine 1004 can identify and providenavigation options for transitioning to patient who share or havediagnostic information in common with the user's patient (e.g., FIG. 29“37 similar patients” at 2902). According to one embodiment, the outcomeengine 1004 can include an analysis component 1014 configured toidentify patients similar to a current patient based on common genomicalterations, affected genes or pathways, disease characteristics,ailment characteristics, treatment characteristics, etc. The analysiscomponent 1014 can be configured to analyze all patient informationavailable on system 1000 to determine matching characteristics, and toprovide the information the UI component 1012 for display to the user.In the cancer setting, similar patients can be identified based onmatches between any one or more of: genomic alterations, affected genesor pathways, treatments, and/or tumor types.

Any identified similar patients can be made accessible by the UIcomponent 1012 through a selectable visual display (e.g., 2902 of FIG.29). For example, a patient information screen can also include a visualindicator for any similar patients identified by the system. FIG. 29 isa screen capture of an example interface 2900. Interface 2900 includes adisplay for “similar patients” 2902 identified by the system. Selectionof the similar patients display can transition the system to treatmentinformation summary displays associated with the similar patients (e.g.,shown in FIG. 30).

As discussed, similar patients can be dynamically determined by theoutcome engine 1004 and/or analysis component 1014. The UI component1012 can generate a visual indicator for the similar patients, which canalso include information on a number of matches identified. Thus, adetermination of similar patients and/or number of matching patients canbe dynamically determined and updated any time the user inputsadditional information regarding treatment and/or outcome.

According to one embodiment, the similar patients indicator isselectable to provide additional detail on similar patient populations.In one example, the UI component 1012 is configured to transition theuser interface to a similar patient display in response to selection ofthe similar patient indicator (e.g., shown in FIGS. 29-30). The similarpatient display can provide additional detail on the similar patientpopulation identified by the outcome engine 1004 and/or analysiscomponent 1014.

According to one embodiment, the similar patient display can includeoptions to filter the similar patient population (e.g., as shown in FIG.30). In one example, the analysis component 1014 is configured toperform filter operations (i.e., reduce the number of matching similarpatients) on the group of similar patients based on user input of filtercriteria. The analysis component 1014 can be configured to matchcharacteristics of a currently viewed patient to any patient sharing thesame characteristics for disease and/or treatment. The characteristicsused to identify similar patients can also be presented by the UIcomponent 1012 as options for further filtering of the similar patientpopulations.

For example, in a cancer treatment setting, the UI component 1012 can beconfigured to display the similar patients with options for filtering onalteration, affected gene or pathway, tumor type, and treatmentprovided, among other options (e.g., see FIG. 30). According to oneembodiment, the system can be configured to present patient populationsand/or outcome information responsive to the specification of variouscombinations of alteration, affected gene or pathway, tumor type, andtreatment. The system can be configured to navigate between differentgroups of patients and respective treatment and outcome data based onuser specification of one or more of alteration, affected gene orpathway, tumor type, and treatment. Navigation can occur betweendifferent views of treatment and outcome data as well as betweendifferent groups of patients that match filter criteria.

According to one embodiment, the user interface includes display optionsfor filtering that provide an intuitive approach for users (e.g.,physicians) to access relevant treatment information, to specify moredetailed filters on the displayed information, generalize or expandtreatment and outcome information, or to include more specific filtercriteria. For example, the user can select specific tumor types thatthey are interested in seeing. In some embodiments, the UI component1012 displays a list of tumor types that appears in the similar patientpopulation and presents those tumor types as options to select in a dropdown list. In one example, the list of tumor types may be determined bythe analysis component 1014 and provided to the UI component 1012 fordisplay.

In other embodiments, genomic alterations in the similar patientpopulation are identified and presented as a selectable drop down list.In yet others, treatments within the similar patient populations areidentified and presented for possible selection as options in aselectable drop down list. In further implementations, genomicalterations, affected genes or pathways, tumor types, and treatmentoptions can be identified from a larger patient population (rather thanlimited to the population of similar patients). In one example, theoptions presented in the user interface for selection can be displayedto include a visual indication reflective that a particular selection isfrom the larger population (i.e., not from the similar patientpopulation).

The similar patient display can include groupings within the similarpatient population, for example, based on the criteria used to identifythe similar patient population. In one example, the patients are groupedby commonality of their respective treatment. Each such group can bepresented in the similar patient display, for example, ordered based onthe number of patients within each group. The group display can alsoidentify the respective treatment common to the group members.

In some embodiments, the UI component 1012 is also configured to respondto selection of the patient groups or the identified treatmentassociated with each group. In response to selection of a group, the UIcomponent 1012 is configured to display additional information regardingthe selected group. For example, the additional information can includeoutcome information associated with the group of patients. Shown inFIGS. 15-31 is a collection of user interface captures including asimilar patient display and a patient group outcome display that can bepresented responsive to selection within a similar patient display of agroup of patients. The patient group outcome view can also be presentedresponsive to selection of a filter, for example, on treatment, where atumor type and genomic alteration type has already been selected.

More generally, the UI component 1012 can be configured to enablesearching within the system to provide access to outcome information.The user can search on one or more of alteration, affected gene orpathway, tumor types, treatment, etc. to identify patient populationsthe user wished to view. In some embodiments, the UI component 1012provides summary displays based on what filter criteria (e.g., searchterms) is defined on the system. In one setting, the filter criteria canbe captured from a currently viewed patient record, and, for example,identification of similar patients can be determined by the system usingcharacteristics of the patient record being viewed. According to someembodiments, the user can also specify the filter criteria for a patientpopulation and outcome/treatment information the user wishes to view. Inother embodiments, the user can also generalize the filter settings onthe system to broaden the view of treatment and outcome data in, forexample, the similar patient display.

In some embodiments, the UI component 1012 presents a plurality offilter criteria as drop down selections (e.g., 3002, 3004, and 3006 ofFIG. 30). Each drop down selection can include an “ALL” setting, whichreflects no filtering on that basis. In some embodiments, the UIcomponent 1012 can also be configured to require that only one of thefilter criteria selections be generalized in order to simplify thevisual display of information.

FIG. 30 is an example user interface 3000 having drop-down menus (e.g.,3002, 3004, and 3006) for specifying filter criteria on a patientpopulation. The patient population display can be accessed via a similarpatient link, where filter criteria can be pre-specified based on thesimilar patient analysis. In another example, the patient populationdisplay can be accessed via selection of an “all patients” tab, and thepopulation specified by selection within any one or more of: 3002-3006.In one example, a generalized selection within a filter can reflect“ALL” when displayed under treatment (e.g., 3008, FIG. 30). Thegeneralized filter criteria can be used by the UI component 1012 togenerate an x-axis of a graphical display, where the y-axis reflects thenumber of patients within each group displayed on the x-axis (e.g.,3010, FIG. 30). The x-axis can be ordered based on a number of patientsand the graphic display sized to fit the number of groups havingmembers. At 3012, the group having the largest number of members “17patients” treated by “vandetanib” is displayed first, at 3014 the grouphaving the next largest membership is displayed “erbitux” “10 patients,”at 3016 the next largest group “erlotinib” “7 patients,” and at 3018“everolimus” with four patients last. Each group can be associated witha link to the group's respective outcome data at 3020-3026. According toone embodiment, the UI component 1012 can also be configured to preventchanging of any other filter criteria to a generalized selection as longas one of the other filter criteria is generalized (e.g., the treatmentcriteria indicates “ALL”).

By specifying a filter selection within a generalized filter category(e.g., FIG. 30 at 3008) the UI component 1012 can be configured totransition to a detail view of outcomes information associated with afully specified group of patients (e.g., view 3100 of FIG. 31 wherefully specified indicates that a specific filter criteria has been inputfor each displayed filter category, for example, at 3102, 3104, and3106). According to some embodiments, the system is configured to fullyspecify the patient group based on specifying alteration, affected geneor pathway, tumor type, and treatment. Within the cancer treatmentsetting, the UI component 1012 can transition to a detailed view of theoutcomes associated with a fully specified treatment group (e.g., tumortype specified, alteration type specified, and treatment typespecified).

In some examples, the detailed view of the outcomes within a treatmentgroup is referred to as an outcome waterfall display. In the outcomewaterfall display (e.g., 3100), each category of outcome available isdisplayed on the y-axis (e.g., 3110—progressive disease, 3112 stabledisease, 3114 partial response, and 3116 complete response), and on thex-axis a vertical bar for each patient (i.e., member of the filteredgroup) is displayed (e.g., at 31A-31Q), where the length of bar on they-axis is configured to show a specific outcome associated with eachpatient. According to some embodiments, the specific outcome shown foreach patient in the waterfall display can be generated based on any oneor more of: the last outcome entered for that patient and thattreatment, an average of the outcomes entered for that patient on thattreatment, a weighted average of outcomes for each patient (e.g.,excluding first and last outcome entries where a change in treatment isindicated), a best outcome entry for the displayed patient, and anoutcome having the longest time period for the patient, among otheroptions.

According to some embodiments, each bar displayed for each patient canbe selected to navigate to additional detail on that patient. In oneexample, selection of a bar in 3100 causes the UI component 1012 totransition to a patient history timeline. The patient history timelinemay be displayed with all of the patient's detail if the selected barand associated patient is one of the user's patients. If the selectedpatient is not one of the user's patients, an anonymized view of thatpatient's treatment over time can be displayed (e.g., as discussed abovewith respect to the patient history timeline). The anonymized view isconfigured to exclude any patient identifying information beyondtreatment, outcome, and disease characteristic (e.g., genomicalteration, affected gene or pathway, tumor type, expression, etc.).

According to one embodiment, the UI component 1012 is configured totransition between patient group displays and detailed outcomeinformation responsive to fully specifying filter criteria andgeneralization of filter categories. The examples above and shown inFIGS. 15-31, are discussed with respect to transitioning between patientgroup displays into detailed outcome information (e.g., outcomewaterfall display) based on specification of a treatment option withtumor type and alteration type already specified in the user interface.In other embodiments, transitions can occur responsive to generalizationand/or specification of an alteration (e.g., by selecting “ANY” in theuser interface) and/or tumor type.

According to some alternatives, generalized patient group views can begenerated and displayed where more than one filter category isgeneralized, or not specified. According to one embodiment, the displayof the associated groups of patients can be re-configured such that thegroupings of patients can include multiple characteristics (e.g.,combinations of specific tumor types and alterations, tumor types andgenes, alterations and treatments, alterations and genes, tumor typesand treatments, and treatments and genes, among other possiblecombinations). In other embodiments, visual displays having multiplegeneralized categories can be generated to illustrated large patientpopulations and, for example, numbers of patients associated with themultiple generalized categories.

According to other embodiments, similar patient information can beaggregated within patient group views according to any display category.In some embodiments, where the system returns small groups of directlymatching patients, the system can aggregate information within thedisplay category to capture further matches. In one example, specificalterations within a patient's cancer are known to be exceeding rare. Insome embodiments, the system can aggregate information based onfunctional similarity, alteration domain, or common pathways to providemeaningful information even for rare alterations.

In one embodiment, patient group views can include informationaggregated within the genomic alterations category for a patient group.In one instance, the information can be aggregated based on classes ofalterations (e.g., alterations in the kinase domain of a gene (e.g.,BRAF) can be grouped separately from BRAF V600E or BRAF V600Kalterations). In some embodiments, information can be aggregated on allBRAF V600 mutations together. In others, information can be aggregatedwithin all of the mutations in an alteration domain (e.g., the kinasedomain) of a gene (e.g., BRAF).

In some examples, an analysis component can aggregate similar patientswithin classes of alterations (e.g., alterations in the kinase domain ofBRAF can be grouped separately from BRAF V600E or BRAF V600K, or on allBRAF V600 mutations together or all of the mutations in the kinasedomain of BRAF). According to another embodiment, the analysis componentcan aggregate similar patient information based on a functionalsimilarity of identified alterations (e.g., distinct mutations butfunctionally similar in the cancer). In further embodiments, alterationsidentified in patient information can be grouped based on a geneticpathway that is implicated by the alteration. For example, alterationsthat affect the same pathway can be grouped and presented on the systemtogether. Additionally, patients and their associated information can bedisplayed within groupings based on common pathways and/or associatedalterations.

According to one embodiment, the ATP binding pocket domain can includealterations in BRAF G466V and BRAF G469A. The system can usespecification of these alterations (e.g., within the ATP binding pocketdomain) to aggregate information associated with patients. In someembodiments, the aggregated information can be provided in a userinterface display for review and/or comparison.

According to one embodiment, tumor suppressor gene alterations caninclude splice site mutations, frameshift indels, homozygous deletions,or nonsense mutations. In some examples, these inactivating mutations(tumor suppressor alterations) can be aggregated across patients for aspecific tumor suppressor gene or even for tumor suppressor genes inwithin a same family.

According to one aspect, aggregating responsive information can beimplemented to insure that common diagnostic information is availablefor review and consideration. For example, an alteration in a tumorsuppressor gene may be identified for one patient but that specificalteration may not be repeated in another patient. According to oneembodiment, by grouping all of the inactivating tumor suppressormutations/alterations from a specific tumor suppressor (e.g. TP53,BRCA1, BRCA2, etc.) or from tumor suppressors in the same pathway, thesystem enables the comparison of many more patients having related tumorsuppressor alterations. If for example, the data being reviewed waslimited only to a matching alteration and gene combination, it may beunlikely that similar patients would ever be identified, as it is highlylikely that specific inactivating mutations will not be observed again.

An example of a pathway or family that could be use by the system toaggregate information is the homologous recombination deficiency (HRD)pathway tumor suppressor genes. Various embodiments are configured foraggregating different inactivating mutations in the same gene orinactivating mutations in different genes in the same pathway. Thesystem can present various views of patient information according to anyof the information aggregates.

In some embodiments, alterations can be aggregated by genes in the samepathway, including for example, the PI3K/mTOR pathways. The system canbe configured to aggregate alterations in PIK3CA, PTEN, PIK3R1, AKT1,AKT2, and other genes in the PI3K/mTOR pathways to increase the numberof patients to compare on, for example, respective therapeuticresponses.

In further embodiments, alterations can be aggregated by genes in thehomologous recombination deficiency (HRD) pathway. The system canidentify and aggregate responsive information for inactivating mutationsin tumor suppressor genes such as: BRCA1, BRCA2, ATM, ATR, FANCA, FANCE,and others. In one embodiment, the aggregated information can bedisplayed by the system to a reviewing physician as potentially beingbiologically and therapeutically equivalent.

According to one embodiment, the outcome engine 1004 can include aconnection component 1016 configured to access and display contactinformation for displayed patients and/or displayed treatment/outcomeinformation. In some embodiments, the contact information provided bythe contact component 1016 is configured to connect to the physiciancaring for a particular patient, or in another example, a manager for aclinical trial.

According to one aspect, the system 1000 and/or the connection component1016 is configured to facilitate collaboration between medicalpractitioners to advance the quality of care provided. For example, theconnection component 1016 can be configured to provide a communicationplatform between registered users of system 1000. The connectioncomponent 1016 can provide for instant messaging, e-mail, or other chat(video or text) capabilities. In some embodiments, the connectioncomponent 1016 can be configured to provide contact information onrequest. The connection component 1016 can also be configured to allow auser to specify whether their contact information should be provided bythe system 1000 when requested.

System 1000 is discussed with respect to example functions andoperations that can be performed by specialized components or engines.System components are intended to include computer based instructionsthat perform operations on a computer system while being executed by oneor more processors, for example, as discussed with respect to system1400 and/or 1402. Various embodiments discussed can include one or morecomponents that provide for the specific functions or operationsdescribed herein. In other embodiments, any one or any combination ofthe functions and/or operations described can be performed moregenerically by the system alone or the outcome engine itself.

Example System

FIG. 11 shows an example embodiment of an outcome tracking and analysissystem 1100. According to one embodiment, system 1100 can implement anoutcome engine 1104 executing on an application interface system 1102 toprovide the functions and operations discussed above with respect tosystem 1000 and/or outcome engine 1004. Outcome engine 1104 can includea plurality of system components. For example, the outcome engine 1104can include a reminder component 1106 configured to request updates onpatient information from associated users. The outcome engine caninclude an input component 1108 specifying categorizations of treatmentand/or outcome information used by the outcome engine 1104 and/orapplication interface 1102. The outcome engine 1104 can also include aUI component 1110 configured to generate user interface displaysrendered by the application interface to end users. The UI component1110 can be further configured to generate displays including outcomeinformation associated with specific treatments and/or patients andgenerate visual options for navigating within patient, treatment, andoutcome information. The outcome engine 1104 can also include ananalysis component 1112 configured to identify relevanttreatment/outcome information from known patient populations. In someexamples, the analysis component 1112 is configured to captureinformation on patient populations from external systems.

In one embodiment, the analysis component 1112 can connect to externalsystems through a communication network 1116. In some embodiments, theanalysis component 1112 can be configured to search publically availableinformation sources to capture information on treatment options and anyassociated outcomes for a given treatment. According to one embodiment,the analysis component 1112 can be configured to search data sourcesconnected to the application interface 1102 via network 1116. Thenetwork 1116 can include any one or more of a LAN, WAN, MAN, virtualnetworks, private network, etc. and may also include, for example, theInternet. For example, the analysis component 1112 can connect to thepublically available ClinicalTrials.gov website 1120 and search fordisease, treatment, and outcome information available from that site.The analysis component 1112 can be configured to analyze any availableinformation source (e.g., PubMed) and store treatment and outcome datainto filterable categories (in one example, tumor type, alteration, andtreatment categories).

According to one embodiment, the analysis component 1112 can process theavailable information into categorized treatment and outcome informationand store the information automatically for use by the outcome trackingand analysis system. According to another embodiment, the analysiscomponent 1112 can provide the treatment and outcome information to anadministrator for review and acceptance prior to use on the system, forexample, prior to storage within database 1118. The analysis component1112 can also connect to other medical service providers or othermedical information sources.

For example, the analysis component can access a genetic testing portal1122. In some embodiments, the application interface 1102 can beintegrated with the genetic testing portal 1122 and can be configured toshare information on patients, diseases, treatments, and outcomes.Information on patients, diseases, treatments and outcomes can also beaccessed from partner outcome data 1124. Partner outcome data sources1124 can include other hospitals or treatment facilities that wish toshare some level of diagnostic information. In some embodiments,partners can contribute treatment and outcome information, whilemaintaining the proprietary nature of other data regarding, for example,their own testing and some specific results on treatment and outcomes.In other embodiments, partner information becomes part of the largerdatabase on outcome and treatment information. Other outcome datasources 1126 can include journal publications, study publications,published articles, etc. In some implementations, the analysis componentcan parse publication data to find and categorize treatment and outcomeinformation for use by the system.

Any such treatment information can be captured and stored for access bythe application interface 1102, for example, in database 1118. Database1118 is illustrated as a single database, but in other embodiments caninclude any storage medium or organizational unit for storing andaccessing treatment and outcome data by a computer system. Furtherembodiments can include a plurality of databases and can also includedistributed data architectures. According to one embodiment, database1118 can include a variety of information used by the applicationinterface 1102 to track and analyze outcome information.

For example, in a cancer treatment setting, genomic testing informationfrom a genomic testing portal can include genomic analysis of apatient's cancer. Genomic analysis can describe genomic alterationspresent in the cancer cells, which can be stored in database 1118 andassociated with a patient and test results. The alteration informationcan provide a basis for determining related analytics on other patientcancers, treatment, and outcome information. Any related analytics canalso be stored in database 1118.

As discussed above with respect to system 1000, the outcome tracking andanalysis system 1100 can facilitate user entry of treatment and outcomeinformation. For example, the outcome engine 1104 can be configured toprovide reminders to user to update patient records with treatment andoutcome information according to system specified categories. The systemspecified categories can be configured to minimize the time a userspends inputting information, while preserving the value of the databeing input for potential diagnostic uses. According to oneimplementation, the system is configured to store, access, and enablenavigation of outcome and treatment information according to alteration,affected gene or pathway, tumor type, and treatment.

The categorized treatment and outcome data input by users can be stored,for example, in database 1118. The stored treatment and outcomeinformation can be use to generate time based summaries of availabletreatment and outcome data, for example, by UI component 1110.

According to some embodiments, the application interface 1102 isconfigured to provide a network accessible portal to medical treatmentand outcome information, including, for example, cancer treatmentinformation. Further, the application interface is configured tofacilitate entry of treatment and outcome information by end users suchthat the time to enter information is minimized, maximizing the benefitsobtained from the collection and analysis of outcome data. Theapplication interface 1102 is configured to accept a variety of endusers. Typically, a user 1130 is a medical professional, including forexample, physicians, physician's assistant, nurses, technicians, etc.The end users can access the application 1102 from a variety oflocations, including, for example, a treatment facility 1132 and ahospital 1134.

In some embodiments, the application interface 1102 can include aconnection component 1114. The connection component 1114 can beconfigured to provide contact information between a plurality of userslocated at disparate hospitals, treatment facilities, etc. In someenvironments, the connection component 1114 can also be configured tomanage communication between users (e.g., provide video chat services,instant message services, e-mail services, etc.). According to oneembodiment, an example goal in providing the connection component 1114includes connecting a physician with another care provider who hasalready pursued one or more courses of treatment with a patient having asimilar tumor, a similar alteration, similar affected gene or pathway,or a similar treatment. In one alternative, the physician can beconnected to a manager of a clinical trial and receive feedback oncourse of treatment, candidacy for the trial, suitability for the trial,among other information.

According to one aspect, by providing the application interface 1102 toa variety of users (e.g., 1130) and simplifying the capture of treatmentand outcome information, the tracking and analysis system 1100 enablescollection of untapped diagnostic information on medical treatment. Inone embodiment, the application interface is configured to facilitatecollection and analysis of cancer treatment and outcome. The collectedinformation and analysis can facilitate daily practice and decisionsmaking by physicians, whether they are located at major metropolitanhospitals (e.g., 1134), treatment facilities (e.g., 1132), or whetherthey are solo practitioners.

In some implementations, data aggregation and analysis can be rooted infilterable organization of all treatment and outcome information toenable easy and intuitive navigation within the treatment and outcomedata. Various embodiments include organization of treatment and outcomeinformation based, at least in part, on alteration information.Alteration information can be provided as a result of genomic testingrelating to a medical condition. In the cancer treatment setting,frequently a multitude of genetic mutations or alterations are presentin cancer cells and will be discerned as results from cancer genomicanalysis. Within the multitude of alterations, one or more alterationscan be associated with a specific patient, tumor type, treatment, and/ortreatment outcome. In some embodiments, the outcome tracking analysissystems can implement a data model organizing all treatment and outcomedata so that all the data is accessible and navigable based onspecification of one or more of alteration, affected gene or pathway,tumor type, and treatment.

In some embodiments, genomic alteration, tumor type, and treatment canbe stored as a tuple in a database. The tuple can be associated withinformation on the affected gene. In some examples, the database caninclude records for tumor type, treatment, and gene/alterationcombinations, stored as a data unit. In other embodiments, the databasecan be indexed on any one or more of alteration, affected gene orpathway, tumor type, and treatment to speed retrieval of outcome dataassociated with those data records. In further embodiments, an outcometracking and analysis system can include a data model based, at least inpart, on organizing patient, outcome, and treatment data usingalteration or affected gene or pathway information.

In some embodiments, the data model can reduce such treatmentinformation to system specified categories for one or more therapiesapplied. For example, data input by a user can exclude dosinginformation, patient demographic information, etc. In other examples,the system can include user interface elements for inputting dosinginformation, patient specific information, etc., as optionalinformation. In further embodiments, the system can request and/orrequire more specific information regarding treatment (dose, frequency,duration, patient weight, height, age, or any other patient factor thatimpacts a dosing regimen).

According to another embodiment, the data model is configured tosimplify outcome information inputs. In one example, the data modeldefines outcome information as one of progressive, stable, partialresponse, and complete response. The user can input outcome informationbased on selection of the defined outcomes, simplifying any data entryby users. Further, treatment and outcome information can be capturedfrom third-party information sources and stored according to the datamodel. According to some embodiments, any data source for treatment andoutcome information can be converted into information retrievable on anyone or more of alteration, affected gene or pathway, tumor type, and aspecified treatment. In further embodiments, additional information ontreatment, outcomes, tumor type, affected gene or pathway, genomicalterations can be stored according to the data model. The additionalinformation can be associated with patients, and accessed from anydefined patient group. In one example, a patient group can be selectedaccording to user input of any one or more of alteration, affected geneor pathway, tumor type, and treatment. The system can enable selectionwithin any specified patient group to access any additional detailinformation associated with any patient with the patient group.

In some embodiments, the system can generate and display outcome andtreatment information according to the data model. For example, visualdisplays organizing treatment and outcome information according togenomic alternation, affected gene or pathway, tumor type and treatmentcan be generated and displayed by the system. The system can beconfigured to respond to selection within of any of the visual displaycategories to navigate or filter within the treatment and outcomeinformation. Selection within patient groups can also triggertransitions to detailed views of treatment and outcome informationassociated with specific patients. (e.g., as shown in FIGS. 29-31).

According to one embodiment, the system 1100 and/or applicationinterface 1102 can execute a variety of processes to capture treatmentand outcome data. FIG. 12 shows an example process 1200 for requestingand capturing treatment and/or outcome information. According to oneembodiment, the process 1200 begins at 1202 with communication of anupdate request at 1202. The update request can specify what informationa user is expected to enter on the system. For example, the request canspecify that treatment information is requested for a patient who hasundergone genetic testing for cancer treatment. The update request canalso specify a request for outcome information associated with patientsof the user. Regardless of the type of request, the update request caninclude links to take the recipient to a web portal foraccessing/inputting such treatment and outcome information.

Process 1200 continues at 1204 with a determination of whether thecurrent user is registered. If user is registered 1204 (YES), the usercan be shown a display at 1206 for inputting treatment and/or outcomedata responsive to entering their user name and password. The displaycan be presented based on any patient requiring an update (e.g., asshown in FIG. 18). If a user is not yet registered 1204 (NO), the usercan be registered at 1205, for example, by providing authenticationinformation to validate the user as a health care provider responsiblefor a patient associated with the update request.

At 1208, the user interface is configured to accept input of treatmentand/or outcome data, for example, entered by a user. Once treatmentand/or outcome data is entered, a patient history display can begenerated at 1210. The patient history display can include treatmentinformation displayed a start point on a treatment timeline. In oneexample, the treatment timeline displays information on a course oftreatment for a cancer and the outcome associated with the course oftreatment over time.

According to some embodiments, input treatment and outcome informationcan be accessed by an outcome engine (e.g., 1004 and 1104) to enablesearching or navigation with patient populations associated with thetreatment and outcome data. For example, the outcome engine can executean example process 1300 for navigating treatment and outcomeinformation. The process 1300 can begin with access to a patient recordat 1302. In some embodiments, information on a currently viewed patient(e.g., alteration, affected gene or pathway, tumor type, and/ortreatment) is used to identify any patients similar to the currentlyviewed patient. At 1304, a similar patient selector can be displayed,for example, in a user interface. Responsive to execution of the similarpatient selector, the currently viewed patient record can betransitioned to similar patient treatment and outcome information. Forexample, the current patient record can be transitioned to a similarpatient population displayed according to any match on genomicalternation, affected gene or pathway, tumor type, or treatment at 1306.

A system executing process 1300 can be responsive to further refinementsor navigation within a set of similar patient results. For example, thesimilar patient population display can include UI elements for furtherrefining the displayed information. If, for example, a user selectsadditional refinements 1308 (YES), any additional specification isaccepted at 1312 and a treatment. Once any new specification ofnavigation criteria have been accepted at 1312, a new set of similarpatients can be generated matching the new criteria. The matchingpatient population can then be displayed at 1314, for example, as adetailed view of treatment and outcome information associated withindividual patients (e.g., FIG. 31).

If no further refinements are desired or specified 1308 (NO) process1300 can terminate at 1310. Process 1300 is shown by way of example, andin different embodiments, can be executed with other orderings or cancombine various steps discussed separately. Further, processes 1300 and1200 can be executed by various computer systems, which can includeoutcome engines and/or the components discussed above with respect tosome embodiments of an outcome engine. In some embodiments, processes1300 and 1200 can be executed by the outcome engine, the outcome enginecomponents, or any combination thereof.

Example Computer Systems

Various aspects, functions, components, and/or processes describedherein may be implemented as hardware, software, or a combination ofhardware and software on one or more computer systems. There are manyexamples of computer systems currently in use. Some examples include,among others, network appliances, personal computers, workstations,mainframes, networked clients, servers, media servers, applicationservers, database servers, web servers, and virtual servers. Otherexamples of computer systems may include mobile computing devices, suchas cellular phones, laptops, tablets, and personal digital assistants,and network equipment, such as load balancers, routers and switches.Additionally, aspects in accord with the present invention may belocated on a single computer system or may be distributed among one ormore computer systems connected to one or more communication networks.

For example, various aspects and functions may be distributed among oneor more computer systems configured to provide a service to one or moreclient computers, or to perform an overall task as part of a distributedsystem. Additionally, aspects may be performed on a client-server ormulti-tier system that includes components distributed among one or moreserver systems that perform various functions. Thus, the invention isnot limited to executing on any particular system or group of systems.Further, aspects may be implemented in software, hardware or firmware,or any combination thereof. Thus, aspects in accord with the presentinvention may be implemented within methods, acts, systems, systemplacements and components using a variety of hardware and softwareconfigurations, and the implementation is not limited to any particulardistributed architecture, network, or communication protocol.Furthermore, aspects in accord with the present invention may beimplemented as specially-programmed hardware and/or software.

FIG. 14 shows a block diagram of a distributed computer system 1400, inwhich various aspects and functions in accord with the present inventionmay be practiced. The distributed computer system 1400 may include oneor more computer systems. For example, as illustrated, the distributedcomputer system 1400 includes three computer systems 1402, 1404 and1406. As shown, the computer systems 1402, 1404 and 1406 areinterconnected by, and may exchange data through, a communicationnetwork 1408. The network 1408 may include any communication networkthrough which computer systems may exchange data. To exchange data viathe network 1408, the computer systems 1402, 1404, and 1406 and thenetwork 1408 may use various methods, protocols and standards including,among others, token ring, Ethernet, Wireless Ethernet, Bluetooth,TCP/IP, UDP, HTTP, FTP, SNMP, SMS, MMS, SS7, JSON, XML, REST, SOAP,CORBA HOP, RMI, DCOM and Web Services.

Computer systems 1402, 1404 and 1406 may include mobile devices such ascellular telephones. The communication network may further employ one ormore mobile access technologies including 2nd (2G), 3rd (3G), 4th (4G orLTE) generation radio access for cellular systems, WLAN, Wireless Router(WR) mesh, and other communication technologies. Access technologiessuch as 2G, 3G, 4G and LTE and future access networks may enable widearea coverage for mobile devices. For example, the network may enable aradio connection through a radio network access such as Global Systemfor Mobil communication (GSM), General Packet Radio Services (GPRS),Enhanced Data GSM Environment (EDGE), Wideband Code Division MultipleAccess (WCDMA), among other communication standards. Network may includeany wireless communication mechanism by which information may travelbetween the devices 1404 and other computing devices in the network.

To ensure data transfer is secure, the computer systems 1402, 1404 and1406 may transmit data via the network 1408 using a variety of securitymeasures including TSL, SSL or VPN, among other security techniques.While the distributed computer system 1400 illustrates three networkedcomputer systems, the distributed computer system 1400 may include anynumber of computer systems, networked using any medium and communicationprotocol.

Various aspects and functions in accord with the present invention maybe implemented as specialized hardware or software executing in one ormore computer systems including the computer system 1402 shown in FIG.14. As depicted, the computer system 1402 includes a processor 1410, amemory 1412, a bus 1414, an interface 1416 and a storage system 1418.The processor 510, which may include one or more microprocessors orother types of controllers, can perform a series of instructions thatmanipulate data. The processor 1410 may be a well-known, commerciallyavailable processor such as an Intel Pentium, Intel Atom, ARM Processor,Motorola PowerPC, SGI MIPS, Sun UltraSPARC, or Hewlett-Packard PA-RISCprocessor, or may be any other type of processor or controller as manyother processors and controllers are available. As shown, the processor1410 is connected to other system placements, including a memory 1412,by the bus 1414.

The memory 1412 may be used for storing programs and data duringoperation of the computer system 1402. Thus, the memory 1412 may be arelatively high performance, volatile, random access memory such as adynamic random access memory (DRAM) or static memory (SRAM). However,the memory 1412 may include any device for storing data, such as a diskdrive or other non-volatile storage device, such as flash memory orphase-change memory (PCM). Various embodiments in accord with thepresent invention can organize the memory 1412 into particularized and,in some cases, unique structures to perform the aspects and functionsdisclosed herein.

Components of the computer system 1402 may be coupled by aninterconnection element such as the bus 1414. The bus 1414 may includeone or more physical busses (for example, busses between components thatare integrated within a same machine), and may include any communicationcoupling between system placements including specialized or standardcomputing bus technologies such as IDE, SCSI, PCI and InfiniBand. Thus,the bus 1414 enables communications (for example, data and instructions)to be exchanged between system components of the computer system 1402.

Computer system 1402 also includes one or more interfaces 1416 such asinput devices, output devices and combination input/output devices. Theinterface devices 1416 may receive input, provide output, or both. Forexample, output devices may render information for externalpresentation. Input devices may accept information from externalsources. Examples of interface devices include, among others, keyboards,mouse devices, trackballs, microphones, touch screens, printing devices,display screens, speakers, network interface cards, etc. The interfacedevices 1416 allow the computer system 1402 to exchange information andcommunicate with external entities, such as users and other systems.

Storage system 1418 may include a computer-readable andcomputer-writeable nonvolatile storage medium in which instructions arestored that define a program to be executed by the processor. Thestorage system 1418 also may include information that is recorded, on orin, the medium, and this information may be processed by the program.More specifically, the information may be stored in one or more datastructures specifically configured to conserve storage space or increasedata exchange performance. The instructions may be persistently storedas encoded signals, and the instructions may cause a processor toperform any of the functions described herein. A medium that can be usedwith various embodiments may include, for example, optical disk,magnetic disk or flash memory, among others. In operation, the processor1410 or some other controller may cause data to be read from thenonvolatile recording medium into another memory, such as the memory1412, that allows for faster access to the information by the processor1410 than does the storage medium included in the storage system 1418.The memory may be located in the storage system 1418 or in the memory1412. The processor 1410 may manipulate the data within the memory 1412,and then copy the data to the medium associated with the storage system1418 after processing is completed. A variety of components may managedata movement between the medium and the memory 1412, and the inventionis not limited thereto.

Further, the invention is not limited to a particular memory system orstorage system. Although the computer system 1402 is shown by way ofexample as one type of computer system upon which various aspects andfunctions in accord with the present invention may be practiced, aspectsof the invention are not limited to being implemented on the computersystem, shown in FIG. 14. Various aspects and functions in accord withthe present invention may be practiced on one or more computers havingdifferent architectures or components than that shown in FIG. 14. Forinstance, the computer system 1402 may include specially-programmed,special-purpose hardware, such as for example, an application-specificintegrated circuit (ASIC) tailored to perform a particular operationdisclosed herein. Another embodiment may perform the same function usingseveral general-purpose computing devices running MAC OS System X withMotorola PowerPC processors and several specialized computing devicesrunning proprietary hardware and operating systems.

The computer system 1402 may include an operating system that manages atleast a portion of the hardware placements included in computer system1402. A processor or controller, such as processor 1410, may execute anoperating system which may be, among others, a Windows-based operatingsystem (for example, Windows NT, Windows 2000/ME, Windows XP, Windows 7,or Windows Vista) available from the Microsoft Corporation, a MAC OSSystem X operating system available from Apple Computer, one of manyLinux-based operating system distributions (for example, the EnterpriseLinux operating system available from Red Hat Inc.), a Solaris operatingsystem available from Sun Microsystems, or a UNIX operating systemsavailable from various sources. Many other operating systems may beused, and embodiments are not limited to any particular operatingsystem.

The processor and operating system together define a computing platformfor which application programs in high-level programming languages maybe written. These component applications may be executable, intermediate(for example, C# or JAVA bytecode) or interpreted code which communicateover a communication network (for example, the Internet) using acommunication protocol (for example, TCP/IP). Similarly, functions inaccord with aspects of the present invention may be implemented using anobject-oriented programming language, such as JAVA, C++, Ada, or C#(C-Sharp). Other object-oriented programming languages may also be used.Alternatively, procedural, scripting, or logical programming languagesmay be used.

Additionally, various functions in accord with aspects of the presentinvention may be implemented in a non-programmed environment (forexample, documents created in HTML, XML or other format that, whenviewed in a window of a browser program, render aspects of agraphical-user interface or perform other functions). Further, variousembodiments in accord with aspects of the present invention may beimplemented as programmed or non-programmed placements, or anycombination thereof. For example, a web page may be implemented usingHTML while a data object called from within the web page may be writtenin C++. Thus, the invention is not limited to a specific programminglanguage and any suitable programming language could also be used.

Examples and Embodiments of a Genomic Portal

It is realized that the adoption and integration of genomic testing intodaily practice faces significant hurdles, in part, based on the abilityto access and the volume of the information that needs to be reviewedand understood in order to facilitate treatment decisions. Further, thecomplexity of the genomic analysis has also limited its potential andsome cases implementation. It is also realized that conventionalapproaches for providing genomic alteration information are not readilyappreciated by the majority of practitioners for their diagnostic value.Nor can the majority of practitioners incorporate such information intoactionable steps to be taken with a given patient.

According to one aspect, it is realized that in order to effectivelyincorporate genomic testing information into daily physician practice,genomic alteration data must be simplified and/or coupled withcontextual applications of the genomic alteration data. In someembodiments, volumes of genomic alterations and associated information(e.g., journal articles, clinical trial information, therapies, etc.)are analyzed and synthesized into actionable information items viewableon an alteration system. According to one embodiment, the system can beconfigured to focus practitioners on discrete portions of the alterationinformation on which they can act.

According to other aspects, curated information is provided on thesystem to enable practitioners to make informed decisions regarding theimplications of the presence of specific genomic alterations. Curatedinformation includes interpretations of available information (e.g.,existing therapies, clinical trials, journals, and publications) forgenomic alterations that may be found in a patient's tumor as a resultof the genomic analysis. The genomic analysis can identify, for example,a tumor type, an affected gene, and an alteration type specific to agiven patient and their cancer. The available information that can becurated can be associated with, and organized by, any of the informationprovided in the genomic analysis (e.g., specific to tumor type, gene,and alteration).

According to one embodiment, the interpretations present contextualinformation regarding the gene implicated in a patient's cancer,including, for example, the expression of the gene, related genes, andcan provide information on related therapies or clinical trials. In someembodiments, the curated information can also include interpretivestatements that summarize and/or apply current analysis of any availableinformation associated with genomic alterations (including, for example,information on an identified gene, information on an identifiedalteration, and information on the patient's tumor). Further, thecurated information can be integrated into a display with genomic testresults, providing intuitive and easy access information sources forunderstanding implication of the test results.

Additionally, the curated information can include references to aninformation source from which the curated information is derived. Insome embodiments, the system can provide direct access to a source ofthe curated information. For example, the system can provide for directnavigation to a relevant clinical trial while in context of reviewinginformation on a specific genomic alteration. The curated informationcan also include direct links to the source information hosted atexternal information sites. (e.g., ClinicalTrials.gov, PubMed, etc.).The information sources can also be reviewed by the user to furtherdescribe or validate the curated information being provided.

By providing such curated information with an easily navigableinterface, a physician or other health care provider may locate the besttreatment information in a timely manner. In some embodiments, theinterface can be organized and navigated based on specific alterationsfound in a patient's cancer. In such settings, the user can navigate toinformation matching the patient's cancer (e.g., tumor type, gene, andalteration) to find directly relevant treatment information.Additionally, the user can navigate to related information matching oneor more of a patient's tumor type, gene, and alteration to inform theuser of potential off-label treatment options.

Genomic testing provides unique opportunities to make more informedtreatment decisions, especially in the field of cancer diagnosis andtherapy development. Some conventional approaches can fail to provideuseable information within the volumes of information provided asresults of genomic testing. Further, it is appreciated that someconventional approaches fail to focus practitioners on actionableinformation within the genomic testing information and any associatedtreatment information.

Accordingly, provided are systems and methods for managing genomictesting information that provide a single reporting source for accessingand applying available information on a patient's cancer. According tosome embodiments, genomic testing on the patient's cancer providesspecific information on the tumor, one or more genes implicated by thetumor, and one or more alterations within the genes. The testinginformation on tumor, gene, and alteration can be used by the system tomanage delivery of curated information that focuses users (e.g.,physicians) on actionable information within the genomic test resultsand associated information. For example, publically available data(e.g., therapy data, clinical trial data, and journal publications) canbe interpreted to provide the curated information based on itsrelationship to one or more of the tumor, gene, and alteration for apatient. The publically available information can be processed on thesystem to provide navigable data structures informing the user ofavailable actionable information associated with a patient's cancer.

According to one embodiment, by providing users an indicator ofactionable information, information within genomic testing reports canbe provided succinctly and enable the users to select the indicator toaccess more detailed information as needed. Further, genomic testresults (e.g., listings of alterations) can be ordered based on thepresence or absence of actionable information items. In one example,actionability of the navigable data structures can be defined onavailable information for an FDA approved agent in the patient's tumortype, available information for an FDA approved agent in another tumortype, and/or available information for a mechanistically driven orbiologically relevant clinical trial based on the alteration(s) found.

The ordering can be configured to focus the user on the actionableinformation to facilitate review of a plurality of alterations and theirassociated information. Indicators of actionable items can be displayedbased on an information source (e.g., a therapy indicator/tag referencesavailable therapy information items related to a genomic alteration, atrial tag references available clinical trial information items, and areference tag for reference information items). The indicator can beassociated with a respective alteration in the plurality of alterationsresulting from genomic testing.

In some embodiments, the system facilitates successive selection ofalterations and associated information within the plurality ofalteration results, for example, using the indicators. By enablingsuccessive selections, the system facilitates better understanding of apatient's cancer and enables more informed treatment decisions.

According to some embodiments, the actionable information includesidentification of FDA approved therapies for a tumor, gene, andalteration combination. Actionable information can also includeidentification of related therapies that are implicated by any one ormore of the tumor, gene, and alteration characteristic of a patient'scancer. According to some embodiments, related therapies can bedetermined by the system and displayed to users to facilitate treatmentdecisions. For example, indicators regarding the related therapies canbe displayed as part of the navigable data structures within userinterface displays generated by the system.

Referring to FIG. 1, there is illustrated an example of a system 100 formanaging genomic testing information using an alteration engine 104.Elements of the system 100 can be provided using a computing system suchas the computer system 500 and/or 502 described with reference to FIG.5. For example, the alteration engine 104 can be executed on thecomputer system 500 and/or 502 to provide the functions and operationsdiscussed herein. In other embodiments, the alteration engine 104 caninclude additional components executed on the computer system to performspecific operations.

As shown in FIG. 1, various embodiments of the alteration engine 104 areconfigured to accept genomic test results 102 and associate the genomictest results with curated information. The curated informing can includedetailed analysis or additional information tailored to thecharacteristic of the test results. For example, the test resultsgenerated for a specific patient can specify a plurality of genes andalterations found within the patient's cancer. The alteration engine 104can be configured to associate curated information tailored to thespecific genes/alteration identified for the patient.

In some embodiments, the alteration engine 104 can be configured togenerate a single source display of the test results, curatedinformation, and any additional information as a dynamic display 106.The dynamic display 106 can include and organize the test results, thecurated information, and the additional information to minimize thevolume of data displayed to the user at any one time. According to oneembodiment, the dynamic display 106 can include a plurality of views ofthe test results, the curated information, and the additionalinformation. In one example, the test, curated, and additionalinformation can be organized into categories for display in a userinterface. In some embodiments, the user interface can be speciallyconfigured for navigation with mobile devices.

The user interfaces generated by the system can also be configured toinclude gene and alteration information specific to a current patientbeing viewed. The user interfaces are configured to present categorizedinformation to facilitate understanding of the gene and alterationinformation for the current patient. In one example, the dynamic displayis presented for a specific patient selected by the user from a patientlisting (e.g. FIG. 6—which can include options for filtering the patientlisting at 650). Once selected, the current patient's information (e.g.,name, date of birth, height, weight, sex, patient id, case id, etc.) canbe provided along with information regarding the genetic testingconducted (e.g., specimen receipt date, report generation date,diagnosis (type of tumor), collection date for specimen, collectionmethod, specimen type, etc.) as a first portion of a dynamic display106.

A second portion of the dynamic display 106 generated by the systemand/or alteration engine 104 can include the results of the genetictesting organized by gene and alteration. In some embodiments, thealteration engine 104 can include a user interface (“UI”) componentconfigured to generate and to provide for navigation within the dynamicdisplay 106. For example, each gene and alteration result generated fromgenomic testing of the current patient's cancer can be displayed as itsown data structure. The data structure can contain selectable indicatorsof actionable information specific to each of the gene/alterationresults. In one embodiment, the UI component is configured to transitionthe dynamic display 106 to the actionable information in response toselection of the indicators.

According to one embodiment, each gene/alteration data structure isreferred to as a brick. Each brick includes a display title or name foran associated gene and alteration. Shown by way of example in FIG. 7, isa section of dynamic display containing a first and second portion (702and 704). The second portion (704) of the display includes thegene/alteration data structures (“bricks”) at 706. Highlighted at 708 isan example brick, which includes a title for a gene/alterationidentified by the genomic testing. The alteration engine 104 and/or UIcomponent can be configured to arrange the bricks responsive toactionable information associated with each brick. For example, brickshaving associated therapy information can be given precedence in adisplay of the test results at 704 over bricks without associatedtherapy information. Further bricks having associated clinical trialscan be given precedence in the display at 704 over bricks withoutassociated trial information. In further examples, the number ofinformation items within each category can be used to establish adisplay precedence based on the categories of actionable information(e.g., therapy, trial, reference). In some embodiments, indicators aregenerated specific to the category of actionable information.

According to some embodiments, actionable information refers to thepresence of information diagnostically relevant to a gene or alteration.For example, actionable information can be reviewed by the user (e.g., aphysician) to inform treatment decisions for that patient, to facilitatethe physician's determinations regarding the patient's cancer, or toeducate the physician on the gene/alteration, among other options. Theactionable information can also be relevant to patient's tumor type aswell as the gene and alteration. As shown, each brick includes anavigable indicator reflecting available actionable information (e.g.,at 712 Therapy indicator and 714 Trial indicator). In one embodiment,the display of bricks can be ordered based on actionability, whereinactionability can be defined on available information for an FDAapproved agent in the patient's tumor type, available information for anFDA approved agent in another tumor type, and/or available informationfor a mechanistically driven or biologically relevant clinical trialbased on the alteration(s) found. In addition, each brick can include atitle display reflecting a specific gene and alteration associated witheach brick (e.g., at 716-717) that can be navigated to additional,and/or actionable information regarding the gene and alteration.

In some embodiments, the brick of information for each gene alterationcan include information on the gene and the alteration, where additionalinformation is visualized responsive to a hover action. In one example,the number of therapies trials and references can be visualizedresponsive to user interface pointer hovering over the gene/alterationbrick.

In some embodiments, actionable information can be grouped by the systembased on categories or source, and indicators can be generated accordingto any such groupings. For example, the system can group information onavailable therapies (e.g., 712 therapy indicator or tag), clinicaltrials (e.g., 714 trial indictor or tag), and in further examples,publications referencing the gene and/or alteration can also be groupedby the system in the dynamic display. Each indicator can be displayedseparately for each brick associated with a gene and alteration. Theindicators are configured to transition the user to one or moreinformation items associated with the displayed gene/alteration. Byselecting the therapy indicator, the user transitions the system tomatching therapy information items. In some embodiments, the brick canalso include an indicator or tag reflecting that updated information isavailable in any one or more of the associated therapy, trial, andreference information items.

According to one embodiment, selection of the indicators (e.g., 712-717)can be configured to cause the alteration engine 104 and/or UI componentto transition the system to additional information specified by therespective indicator. For example, selection of any of 712-717 causesthe system to transition to a third portion of the dynamic display 106(e.g., FIG. 7B (710)). The system can also transition to newportions/pages using jump menu 711. Shown at 710 is an example of thethird portion of the dynamic display 106. As shown, the third portionincludes categorization of the information items associated with thetumor, gene, and alteration information relevant to the currently viewedpatient (including, for example, the genes/alterations shown at 704).According to some embodiments, the information displayed in the thirdportion can be grouped based on system categories for the relatedinformation. In one example, the system categories can include: GenomicAlteration Interpretations (718); Therapy (720); Clinical Trial (722);and References (724). In some embodiments, each drawer can be responsiveto hover, displaying additional information for the drawer being hoveredon.

Shown at 710 are the information categories arranged by associated datastructures. Each data structure in the third portion 710 of the dynamicdisplay 106 can be configured to expand or open upon selection. Further,the data structures displayed can be accessed through the actionableinformation indicators at 712-714 or the gene/alteration indicators at716-717. Common to the data structures in the third portion of thedynamic display 710 is a selectable expansion element (e.g., 726) thatexpands to show the information items contained within the associatedcategory or group. The data structures in the group can be referred toas drawers, where the drawers are configured to open or expand in a userinterface display to provide additional information (e.g., responsive toselection of 726 or actionable information indicators 712-717). Eachdrawer can include an indication of a number of information itemsorganized within the drawer (e.g., at 728).

Shown in FIGS. 7C-D is an expanded view of the Genomic AlterationInterpretation Drawer 718. In the example display, each gene andalteration is associated with interpreted statements that providecontextual information regarding the gene/alteration. The contextualinformation can include, for example, the expression of the gene (e.g.,a resulting protein), related genes, genomic family, etc. Theinterpreted statements can also provide information on frequency of thealteration (e.g., in the general population or a study population),information on related genes/alterations, related therapies, or relatedclinical trials. In some embodiments, the interpreted statements areincluded as “curated” information that summarizes and/or providescurrent medical knowledge and/or analysis of the gene and alteration,whether the knowledge matches the specific tumor type for the patient ornot. The curated information can be generated and stored on the systemfor access by the alteration engine 104 and/or the UI component.

In some embodiments, the alteration engine 104 is configured to generatecurated information from various knowledge bases (e.g.,ClinicalTrials.gov, PubMed, journal publications, etc.). In oneembodiment, the alteration engine 104 can include a curation componentconfigured to capture genomic information for curation. In someembodiments, the alteration engine 104 captures online resources (e.g.,clinical studies, journal publications, research documents, academicarticles/resource, etc.) pertaining to any one or more of tumor, gene,and alteration. The alteration engine 104 and/or curation component canbe configured to present the captured information to a human curator,who creates interpreted statements from the available information. Insome embodiments, the alteration engine 104 can be configured tosummarize or synthesize online resources into automatically generatedinterpreted statements. In one embodiment, the alteration engine 104and/or curation component can be configured to present such interpretedstatements to human curators for approval or editing prior to use on thesystem. In one embodiment, the curation component can automaticallyidentify information items for curation based on keywords (e.g.,keywords for tumor type, gene, alteration, and/or therapy). In someimplementations, the curation component can parse and capture contentfrom the identified information items. The captured content can bepresented to, for example, the human curators for revision and/orapproval.

According to one embodiment, each information item within the drawer(e.g., 718) can include a navigation option to provide further detail ona selected information item. For example, row 730A forERBB3/amplification can be selected in the user interface to transitionthe system to a detailed view of information on the ERBB3 gene andamplification alteration for the patient's tumor type. In anotherexample, the alteration engine 104 and/or UI component can generate ahyperlink or other navigable element provided in the dynamic display(e.g., at 732) to transition the system to the detailed view. Shown inFIG. 7E is an example detailed view of the gene/alteration/tumorcombination. The detailed view can include the interpreted statementsshown for the gene and alteration. Further, the detailed view can alsoinclude navigation options for transitioning the system to relatedgenomic information. Shown at 734-738 are expandable display elements.Responsive to selection, the expandable display elements can each beindependently expanded to provide navigation options. Each navigationoption can be grouped according to a respective information source. Insome embodiments, the expandable display elements 734-738 can include anindicator of a number of information items within each group (e.g., at740).

Shown in FIG. 7F is an expanded view of each expansion element 734-738.Each expansion element provides access to a related information sourcebased on the respective grouping (e.g., 734, related therapy, 736,related trial, and 738, related references). In some embodiments, therelated therapy group 734 can include therapies that match the patient'stumor type, gene, and alteration as well as therapies that match withany one or more of the three options. In other embodiments, relatedinformation can be included in any of the displayed groups 734-738, forexample, when the information source matches any one or more of thetumor, gene, and alteration of the current patient.

According to some embodiments, the alteration engine 104 is configuredto identify related information for inclusion in the dynamic display 106and associated views. In one example, the alteration engine 104 caninclude an analytic subsystem configured to identify matches betweentumor type, gene, and/or alteration and includes the matchinginformation items according to display drawers (e.g., at 710).Identification of related information by the analytic subsystem can beemployed by the alteration engine 104 and/or the UI component togenerate the indication of the number of information items associatedwith each display drawer (e.g., at 728) and/or in the detailed viewexpandable elements (e.g., at 740). In some examples, the analyticsubsystem and/or alteration engine 104 can maintain counts for eachinformation item within system categories (e.g., therapy, trial,references) and store that information for access within each patient'sgenomic test report or in a detailed information screen (e.g., at 740).

As discussed, once expanded the expansion elements 734-738 providenavigable links to further detailed information. At 742, provided is anavigable link to a detailed therapy view. In response to selection of742, for example, in a user interface, the alteration engine 104 and/orUI component causes the system to transition to a detailed view of thePerjeta related therapy. The related trials links at 744-746 and therelated references links at 748 are configured to transition the user toexternal information sources. For example, the related trials links at744 and 746 are directed to respective clinical trial informationsources maintained on the ClinicalTrials.gov website. In anotherexample, the related references links at 748 are configured totransition the user to respective publications maintained at PubMed.gov.In some embodiments, the transition to the external information sourcesis executed by causing a browser to open a new window or a new tab. Thealteration engine 104 and/or UI component can be configured to maintainan active session, for example, in a browser while the user is reviewingexternal information sources in the new window or tab.

Shown in FIG. 7G is an example detailed therapy view. As discussedabove, the detail therapy view can be accessed responsive to selectionof 742. The detailed therapy view can also be accessed from aninformation item display provided with in the therapy drawer 720(discussed in greater detail below). According to some embodiments, thedetailed therapy view describes the details of the therapy, for example,the drug perjeta. The details for the therapy can also includeinformation on the timeframe associated with the descriptive information(e.g., last updated information), which be used by the system to trackupdates to therapy information. In some embodiments, detailedinformation for a therapy can include description of any FDA approveduses of the therapy (“on-label” uses). In further embodiments, approveduses can be accompanied by therapy target information and/or rationalfor applying the therapy to a tumor, gene, and/or alteration. Thetarget/rational information can include interpretive statements, whichprovide insight into how the therapy is related to a patient, and morespecifically to the patient's tumor, gene, and/or alteration.

In the example display of FIG. 7G, illustrated are expansion elementssimilar to the expansion element of the detailed view of agene/alteration/tumor combination. According to some embodiments, theexpansion elements for Related Trials and Related References (e.g., 752and 754) can overlap or include the same information sources. In otherembodiments, additional information sources can appear as links ineither category relative to the detailed view of thegene/alteration/tumor combination. At 750, Related Alterations aredisplayed as part of the detailed treatment view. Once expanded, therelated alterations can include a navigable link 756 directed back tothe detailed view of the gene/alteration/tumor of FIG. 7F. In otherembodiments, if more than one alteration is matched to perjeta (forexample, by the analytic subsystem) additional navigable links would bedisplayed under 750. As discussed, the user can navigate through apatient's test results and the associated information through a varietyof paths.

For example, returning to FIG. 7B, drawer 720 can be selected totransition the dynamic display to an expanded view of Therapy drawer720. Shown in FIG. 7H is an example view of an expanded Therapy drawer.According to one embodiment, within the therapy drawer are all availabletherapies associated with a patient's cancer. The associated therapiescan be identified, for example, by the alteration engine 104 and/or theanalytic subsystem based on matching a gene or alteration within thepatient's tumor type or in other tumor types. The therapy informationitem display within the drawer (e.g., at 756) can include anidentification for the therapy (e.g., drug name, name of a treatmentprocedure, combination of drugs, etc.) at 760, the gene (e.g., from thepatient's test results) associated with the therapy at 762, thealteration type for the gene at 763, and indicators for whether thetherapy has been approved by the FDA within the patient's tumor type at764, and identification of any tumor types for which the therapy has FDAapproval (if any) at 766.

In some embodiments, the gene name and the alteration type identifiedcan also be used to access detailed information views for either thegene or alteration type. For example, 762 and 764 can be selected in auser interface to transition the system to detailed view of thegene/alteration/tumor combination show in FIG. 7E and to the detailedtherapy view shown in FIG. 7G, respectively. According to someembodiments, providing information on FDA approved therapies within apatient's tumor type facilitates on-label uses of approved therapies. Infurther embodiments, providing information on FDA approved therapiesoutside of the patient's tumor type provides valuable insight intopotential off-label uses, and can facilitate the user's decision makingon related but not labeled use of a therapy.

According to some embodiments, the dynamic display is configured forsuccessive navigation through the patient's genomic alterations and theinformation associated with the patient's genomic alterations. In oneexample, the user can expand the clinical trial drawer 722 to navigatewithin the clinical trial information related to the patient's cancer.The user can expand the drawer 722 as an initial selection, or, forexample, after viewing information in other drawers. Responsive toselection of the drawer 722, the alteration engine 104 and/or UIcomponent causes the system to transition the dynamic display to anexpanded view of the clinical trial drawer 722 (e.g., shown in FIG. 7I).

FIG. 7I shows a portion of an example view of the clinical trial drawerin an expanded state. As shown, only 2 of 9 matching clinical trials areillustrated in the portion of the example view. Each information item(e.g., 768 and 770) within the clinical trial drawer can include commonelements. According to one embodiment, the common elements can include aclinical trial identifier 772, which can be selected in the userinterface to transition the user to an external information source, forexample, ClinicalTrials.gov. In one example, the alteration engine 104can be configured to transition the user to the external informationsource through a new browser window or through a new tab opened in abrowser program. By opening new windows and/or tabs the user is readilyable to transition back to the dynamic display 106 and any viewcurrently shown.

In some embodiments, the common element can also include a rationalindicator associated with the clinical trial being display. Responsiveto selection of the rational indicator at 774 the rational associatedwith the clinical trial can be displayed as text in an overlay display(e.g., as shown in FIG. 7J, 777). The rational can include specificidentification on how the information was obtained (e.g., keywordsearching on clinicaltrials.gov including the keywords searched). Insome embodiments, the system can provide a link (not shown) associatedwith the search terms to take the user to the source and the searchresults obtained. Selection of a close window indicator (e.g., 778)returns the dynamic display to the expanded view of the clinical trialdrawer. Other common elements shown in the information items (e.g., 768)can include one or more of: targets associated with the clinical trials(e.g., “Aurora kinase” at 780, a phase associated with the clinicaltrial at 781, therapies at 784 (if any), location information for theclinical trial at 786, and status for the clinical trial (e.g.,recruiting).

In some embodiments, the clinical trial drawer can include filter optiondisplays. The filter operation displays can be configured to acceptpatient specific criteria (e.g., height, weight, age, tumor type, gene,alteration, sex, prior treatment, current diagnosis, prior outcome,etc.) to return clinical trial information items that match the inputcriteria.

Once the user has reviewed any clinical trial information she wishes tosee, the user may proceed to review references related to the patient'scancer. According to one embodiment, the user can select the referencesdrawer 724 to cause the system to transition the dynamic display 106 toan expanded view of the reference drawer 724. For example, a portion ofan expanded view of the reference drawer 724 is shown in FIG. 7K. Eachinformation item with the reference drawer (e.g., 788-794) can includecommon elements. According to one embodiment, the common element caninclude a name for the reference at 796, which can include the authorsof the reference, the title of the reference, and associatedbibliographic information for citing to the reference. Additional commonelements can include a link to the reference, for example, at 798.Selection of the link can cause the system to transition to thereference, which may be hosted at a location external to the system. Asdiscussed above, external transitions can be provided through newbrowser windows and/or tabs, to allow the user to maintain a sessionwith the system.

As discussed above, the dynamic display 106 is configured to providemultiple paths to genomic alteration information, actionableinformation, and specific information items or views. In someembodiments, the path taken through the dynamic display 106 can impacthow the system displays any information within a given view. Forexample, expansion of one of the drawers at 718-724 provides access tothe information items within each group. According to one embodiment,successive selection of another drawer can be configured to close anyopen drawer as well as to transition the dynamic display to the expandedview of the selected drawer. Further, responsive to selection of adrawer within the dynamic display, each information item within aspecific drawer is presented. If the information items within a drawerare accessed from a link (e.g., 712) displayed in a brick (e.g., at 706)from the second portion of the dynamic display (704), then theinformation items associated with the link (i.e., therapies associatedwith the ERBB3 gene are highlighted to facilitate review). The systemand/or alteration engine 104 can be configured to highlight suchassociated information items within any drawer accessed (e.g., 718-724)when shown in their respective expanded views.

According to some embodiments, additional drawers can be provided in thedynamic display 106. In one implementation, the third portion of thedynamic display can include an update drawer 800 shown in FIG. 8A. Theupdate drawer 800 organizes updates to any information item presented ina patient report. In some embodiments, the alteration engine 104 isconfigured to track updates to any information item (e.g., updates togenomic alteration interpretation, new genomic alterationinterpretations, revisions to genomic alteration interpretations, newtherapies, new approvals for therapies, revisions to approved therapies,new clinical trials, new results for clinical trials, new publications,references, retractions for references, etc.). In some examples, thetracked updates can be organized and presented in an update drawer(e.g., 800). In additional examples, the tracked updates can beidentified with a visual indictor (e.g., 802) for a respective drawerhaving updated information. Each visual indicator for any updates caninclude information on a number of respective updates (e.g., 803).

In some embodiments, the alteration engine 104 can include an updatecomponent configured to track updates to information items associatedwith a patient's test report. The update component and/or the alterationengine 104 can also be configured to maintain information on the lasttime a report was accessed to determine what updates have occurred sincea last view. The update component can be configured to present suchupdates within an update drawer. Further, the update component cangenerate an indicator for each drawer containing updated information(e.g., 802).

Shown in FIG. 8B is an additional view of updates information tracked bythe system. FIG. 8B illustrates an updates timeline view accessed, forexample, in response to selection of an updates tab at 806. According toone embodiment, the updates timeline view organizes and displays anyupdates to information items associated with a patient report accordingto a date for the respective the update. The updates timeline view canalso be configured to organize the update information items responsiveto categorization. For example, control element can be displayed as partof the updates timeline view at 808. Responsive to selection of 810Interpretations, 812 Therapies, 814 Trials, and 816 References, updatesfor information items in each group will be presented at the top of theupdates timeline display. FIG. 8D shows another embodiment of an updatestimeline display. Some embodiments of the updates timeline display caninclude a control 818 configured to cause the system to display or hidefilters for narrowing or expanding the number of updated informationitems in the display. Example filters displayed by the system include:update categories at 820, update types at 822, and a temporal filter ondisplayed updates at 824. Selection within one or more of the filterscan be configured to limit the update information items displayed toonly those update items matching the filter criteria.

Selection of the displayed updates (e.g. 823 FIG. 9A or 809 FIG. 8C) canbe configured to transition the user interface to a detail view of theselected update (e.g., FIG. 8C illustrates a detail view 817 for an EGFRalteration providing information on updates, interpretation, frequencyof occurrence, overview information, and relevance to targetedtherapies). FIG. 8C can include a selectable option to display aninterpretation update history (e.g., 819), where all changes to aninterpretation for an alteration can be displayed. Each display drawer(alteration, therapy, trial, and references) can have an updates viewfor each information item within the respective drawers that provideinformation on any updates to a respective information item. Accordingto another embodiment, the alteration engine 104 can also be configuredto compiled genomic test results and any associated information intostatic test reports 107. For example, a static test report 107 can begenerated by the alteration engine 104 in response to selection of adownload control. According to one embodiment, the static report reflectthe same organization as the dynamic display 106, however, the staticreport differs in that all of the associated information reflects theexpanded views of each category of associated information (e.g.,expanded views of drawers 718-724). An example static report 107 isshown in FIGS. 9A-9N. In further embodiments, users can register toreceive static or physical reports that are delivered via mail or fax.In some examples, the user does not access the system to retrievegenomic test results rather the results are delivered as a physicaldocument.

According to one embodiment, the static report can include patientdemographic information (e.g., 902—date of birth, gender, case #,medical record #, and id). The static report can also provide summaryinformation on the information contained in the report (e.g., at904—summary of the genomic alterations found, therapy associated withclinical benefit, therapies associated with lack of response, andclinical trial information, as well as page references for accessingdetailed information). In one example, the static report can includesummary information on therapies (e.g., at 906—genomic alterationsdetected, FDA approved therapies (in patient's tumor type), FDA approvedtherapies (in another tumor type), and potential clinical trialsorganized by alteration). The static report can include information ongenomic alterations at 910 of FIG. 9B-C, detailed information ontherapies (e.g., 912), clinical trials to consider at 914 of FIGS.9E-91. The static report can also include information on referencesrelied on to generate the report at 916 of FIGS. 9J-9M. In one example,the static report can also include information on the genetic testingperformed on the patient and include information on how the reportshould be utilized (e.g., at 918).

Example Genomic System

Show in FIG. 2 is an example embodiment of a system 200 for managinggenomic testing information. The system 200 can be configured to providea single reporting source for accessing and applying availableinformation on a patient's cancer. According to some embodiments,genomic testing on the patient's cancer provides specific informationthe tumor, one or more genes implicated by the tumor, and one or morealterations within the genes which can be displayed by the system 200through a web interface 202. In some embodiments, the web interface 202can include an alteration engine 204 that performs any of the operationsdiscussed above with respect to the alteration engine 104. For example,the web interface and/or alteration engine 204 can be configured to usethe testing information on tumor, gene, and alteration for a patient tomanage delivery of curated information to end users (e.g., technicians,physicians, medical personal, etc., at 205) over a communication network216. In one embodiment, the alteration engine 204 can include a UI ornavigation component 212 configured to generate displays that focususers (e.g., physicians) on actionable information within the genomictest results and associated information. For example, the UI component212 can display navigable data structures including information on genesand alterations identified in a genomic test coupled with indicatorsinforming the user of available actionable information associated with apatient's cancer.

According to some embodiments, the alteration engine 204 can includespecific component for provide specific functionality on the webinterface 202. For example, the alteration engine 204 can also include areport generator component 206 configured to generate physical and/orstatic report for downloading through the web interface (e.g., shown inFIGS. 9A-9N). The alteration engine 204 can also include an analyticsubsystem 208 an analytic subsystem configured to identify matchesinformation between a current patient's tumor type, gene, and/oralteration and include or identify the matching information items fordisplay in the patient's test results.

According another embodiment, the alteration engine can also include acuration component 210 configured to generated curated information foruse on the system. The curated information can include interpretedstatements regarding any one or more of genomic alterations, animplicated gene, a patient's tumor type, and/or potentially applicabletherapies for a patient's cancer. In some examples, the curationcomponent can be accessed by human operators “curators” who generateand/or approve system generated interpreted statement regarding genomicalterations, an implicated gene, a patient's tumor type, and/orpotentially applicable therapies.

As discussed, the alteration engine can also include the UI component212 configured to generate and display navigable data structures (e.g.,bricks and drawers) which include information on genes and alterationsidentified in a genomic test, which can be coupled with indicators foractionable information associated with a patient's cancer. The UIcomponent 212 can transition the system to the actionable information(e.g., therapy information items, trial information items, referenceinformation items) responsive to selection in the user interface.

In further embodiments, the alteration engine can include an updatecomponent 214 configured to track any updates to genomic alterations andany information associated with the genomic alterations. In oneembodiment, the update component 214 can identify updates informationfor display by the UI component 212. Various embodiments, of thealteration engine components are configured to perform the function andoperations discussed above with respect to the alteration engine 104 andassociated components.

According to some embodiments, the web interface 202 can be accessed byusers (e.g., 205) over the internet. The user can access the webinterface from a variety of location (e.g., laboratory 218, hospital220, and treatment facility 222). In various embodiments, the users atany one or more of 218-222 can share genomic test reports with eachother. For example, the web interface 202 can be configured to providesocial functions between users. In some embodiments, the web interfacecan limit sharing to practice groups, within treatment facilities, orwithin medical institutions (e.g., hospitals). According to one aspect,sharing of test results and associated genomic information on patientscan create a strong community of physicians, and foster discussion abouttreatment or even specific patients.

According to some embodiments, the web interface 202 stores genomic testinformation in database 217. Database 217 is illustrated as a singledatabase, but in other embodiments, database 217 can include any storagemedium or organizational unit for storing and accessing genomic testresults and associated information. Further embodiments can include aplurality of databases and can also include distributed dataarchitectures. According to one embodiment, database 217 can include avariety of data records accessed by the web interface 202 to managedelivery of genomic test results and associated information.

For example, the database can include information on genomic testing. Inone example, genomic test results are stored and associated with patientrecords. The genomic test results can include information on genomicalterations. Specific genomic alterations can be stored in database 217and access for presenting information within a display of a patient'stest report. The database can include curation records stored andassociated with any one or more of a tumor type, gene, and/or genomicalteration. Information on clinical trial can likewise be stored asinformation items associated with any one or more of a tumor type, gene,and/or genomic alteration. The database 217 can also store therapyinformation and references information and provide associated for eitherto any one or more of a tumor type, gene, and/or genomic alteration. Thedatabase 217 can also be configured to track and store information onupdates to any information within the database. In one example, updatescan be flagged by other system components and the flags resolved orremove once viewed.

In further embodiments, the database can store information on data viewsfor used by web interface and/or the UI component 212. The views caninclude, for example, alteration views, genomic interpretation views,clinical trial views, therapy views, static report views, patient recordviews, references views, and updates views. Each one or more of theviews can be accessed and used by the web interface to presentinformation on genomic testing and associated information to a user. Insome examples, the system and/or web interface can be configured tocapture information from external information sources for storage indatabase 217. In one example, external data source 224 can containinformation related to a patient's tumor type, gene, and/or alteration.The information from the external information can be captured and storedas records in database 217 accessible via the relationship to the tumortype, gene, and/or alteration.

According to some embodiments, the information stored in database 217can include reference to the external information source. For example,clinical trial information items can include links to clinicaltrials.gov226, reference information items can include links to PubMed.gov (e.g.,228). In further embodiments, the web interface 202 can be configured toaccess genomic alteration information for cancer diagnoses made at ahospital or laboratory (e.g., 230). For example, the web interface cancapture genomic information from EMR (electronic medical records) toretrieve tumor type, implicated gene, and/or alteration type for storagein database 217. In some implementations, references or links to thespecific medical records can also be stored in the database. In oneexample, the links to the medical records can be presented in a dynamicdisplay generated on system 200.

According to one aspect, the database 217 and all associated informationcan be organized or accessed based on one or more of tumor type, gene,and alteration. In one embodiment, the tumor type, gene, and alterationdata is stored as a data unit (e.g., a tuple). The data unit can be usedby the system to identify or display related information based onmatching any one or more of the tumor type, gene, and alteration. Infurther embodiments, each data unit can be linked to actionableinformation (where it exists). For example, each data unit can be linkedto a matching therapy (e.g., a therapy information item describing aspecific therapy, application, etc.). In another example, data units canbe linked to a matching clinical trial (e.g., stored as a clinical trialinformation item).

According to one embodiment, associated of all the information in thedatabase according to tumor, gene, or alteration provides insight intoprescribed uses of therapies (on-label) and off-label applications forsuch therapies. In one example, off-label used can be identified basedon alteration (e.g., different tumors but same alteration—providesrelation information on a potentially effective therapy the currentpatient's cancer.

According to another embodiment, each record can be associated with adata space for an update flag. Responsive to any update to informationon the database 217, the system can enter information in the data spacefor the update flag. Tracking updates to genomic alteration andassociated information facilitates user awareness of potentialsignificant changes in a patient report. Further, tracking of updateinformation in the database 217 enables the system to delivernotification regarding any updates.

In some further embodiment, social functions can have associated recordsin the database. For example, permission information (e.g., who canshare a report and/or who can receive a shared report) can be associatedwith test reports stored in database 217.

According to some embodiments, the web interface 202 can implement avariety of function and processes for managing delivery of genomic testresults and any associated information. FIG. 3 shows an example processflow 300 for managing genomic testing information. The process 300begins at 302 with access to genomic test results. According to oneembodiment, genomic test results include information specific to apatient's tumor type, one or more genes implicated by the tumor, andalteration type associated with the one or more gene. At 304, the tumortype, gene, and alteration combinations for the patient's cancer areanalyzed, and relevant information items are identified at 306.

In some embodiments, the relevant data items can include clinical trialsthat match on any one or more of tumor type, gene, and alteration. Therelevant data items can also include therapies or references that matchon tumor, gene, and/or alteration. In some example, the relevant dataitems are stored for analysis at 304 based on activity of curators. Inone example, human curators can review clinical trial information (e.g.,criteria, gene/alteration target, trial therapy, trial drug) andassociate that clinical trial information with tumor types, genes,and/or alterations. The human curators can also review and characterizeinformation on therapies and reference for use in, for example, process300.

Once relevant information is identified, for example, at 306, anyrelevant information item can be associated with the patient having thematching tumor type, gene, and/or alteration at 308. The association(s)defined at 308 can be used at 310 to generate navigable data structureswhich can be configured to organize gene and alteration combinations andlinks to any associated relevant information (e.g., identified at 306and associated at 308). In some embodiments, the navigable datastructures can be presented in user interface display

In other embodiments, the relevant information identified at 306 can beassociated with patient records and/or specific genomic tests at 308based on a specified data model. Further, association of the relevantinformation at 308 can include generation and storage of the associatedinformation a data unit (e.g., information item) and the data unit canthen be associated with the patient, and/or a gene or alteration in thepatients genomic test results through a navigation link. The navigationlink can be used as part of a dynamic display for a specificgene/alteration combination. Responsive to selection of the link, thedynamic display can transition to the relevant information.

FIG. 4 shows an example process 400 for navigating through genomictesting information. The process 400 begins at 402 with generation ofnavigable data structures. In some embodiments, the navigable datastructures can be generated by other processes (e.g., process 300) andaccessed at 402 rather than being generated at 402. The navigable datastructures can be generated or accessed based on genomic test resultsfor a current patient. In one embodiment, a genomic data structure isgenerated or accessed for each genomic alteration identified in thecurrent patient's cancer cells. In other embodiments, navigable datastructures can be accessed or generated for any associated informationrelevant to each genetic alteration at 402. In some examples, theassociated information can include relevant therapies, relevant clinicaltrials, and/or relevant references.

At 404, each genomic data structure is displayed. The genomic datastructures can be displayed in a first portion of a user interface. Eachof the genomic data structures is configured to access associatedinformation relevant to the genomic alteration stored as part of thegenomic data structure. For example, each genomic data structureincludes specification of a gene (e.g., by name) and an alteration typefor the gene found in the patient's cancer cell. At 406, responsive toselection of one of the genomic data structures, the user interfacetransitions to an associated information display area. In someembodiments, the associated information display area can includeorganization of associated information data structures by informationtype. In some examples, the organization by information type includesdrawers for each type configured to expand upon access to the contents(and type) organized within the drawer. Depending on the selectionwithin the genomic data structure, the transition to the associatedinformation display area can include a transition to a specific categoryof information (e.g., genomic alternation interpretations, therapies,clinical trials, references, and updates). Within the associatedinformation display area, associated information data structures aredisplayed at 408.

Each of the associated information data structures can also benavigable. Responsive to selection of the associated information datastructures, the user interface can transition to additional informationon the selected associated information data structure. The transitioninvoked depends on the source/target of the associated information datastructure. If the associated information structure includes an externaltarget, for example, an external website, selection of the externalinformation source at 410 YES, results in a transition of the userinterface to the external site at 412. In one example, the external sitecan include ClinicalTrials.gov or PubMed.gov, among other options.

If the target of the associated information data structure is notexternal 410 NO, selection of the associated information data structureresults in a transition to a detailed view of the associated informationat 414. For example, depending on the associated information datastructure and/or a target selected within the structure, the transitioncan be made to a detailed view of therapy information (e.g., FIG. 7G) ora detailed view of a gene/alteration combination (e.g., FIG. 7E).

According to some embodiments, process 400 is intended for successiveexecution to transition between and within genomic data structures,associated information data structures, detailed views, and externalinformation locations. For example, steps 406-408 can be repetitivelyexecuted for each one of a plurality of genomic data structures and/orsteps 408-414 can be repetitively executed to access each one or some ofa plurality of associated information data structures.

Further, either process 400 or 300 can be executed on various systems orcan be executed by various system components.

Example Computer Systems

Various aspects, functions, components, and/or processes describedherein may be implemented as hardware, software, or a combination ofhardware and software on one or more computer systems. There are manyexamples of computer systems currently in use. Some examples include,among others, network appliances, personal computers, workstations,mainframes, networked clients, servers, media servers, applicationservers, database servers, web servers, and virtual servers. Otherexamples of computer systems may include mobile computing devices, suchas cellular phones and personal digital assistants, and networkequipment, such as load balancers, routers and switches. Additionally,aspects in accord with the present invention may be located on a singlecomputer system or may be distributed among one or more computer systemsconnected to one or more communication networks.

For example, various aspects and functions may be distributed among oneor more computer systems configured to provide a service to one or moreclient computers, or to perform an overall task as part of a distributedsystem. Additionally, aspects may be performed on a client-server ormulti-tier system that includes components distributed among one or moreserver systems that perform various functions. Thus, the invention isnot limited to executing on any particular system or group of systems.Further, aspects may be implemented in software, hardware or firmware,or any combination thereof. Thus, aspects in accord with the presentinvention may be implemented within methods, acts, systems, systemplacements and components using a variety of hardware and softwareconfigurations, and the implementation is not limited to any particulardistributed architecture, network, or communication protocol.Furthermore, aspects in accord with the present invention may beimplemented as specially-programmed hardware and/or software.

FIG. 5 shows a block diagram of a distributed computer system 500, inwhich various aspects and functions in accord with the present inventionmay be practiced. The distributed computer system 500 may include one ormore computer systems. For example, as illustrated, the distributedcomputer system 500 includes three computer systems 502, 504 and 506. Asshown, the computer systems 502, 504 and 506 are interconnected by, andmay exchange data through, a communication network 508. The network 508may include any communication network through which computer systems mayexchange data. To exchange data via the network 508, the computersystems 502, 504, and 506 and the network 508 may use various methods,protocols and standards including, among others, token ring, Ethernet,Wireless Ethernet, Bluetooth, TCP/IP, UDP, HTTP, FTP, SNMP, SMS, MMS,SS7, JSON, XML, REST, SOAP, CORBA HOP, RMI, DCOM and Web Services.

Computer systems 502, 504 and 506 may include mobile devices such ascellular telephones, tablets, touch screen devices, etc. Thecommunication network may further employ one or more mobile accesstechnologies including 2nd (2G), 3rd (3G), 4th (4G or LTE) generationradio access for cellular systems, WLAN, Wireless Router (WR) mesh, andother communication technologies. Access technologies such as 2G, 3G, 4Gand LTE and future access networks may enable wide area coverage formobile devices. For example, the network may enable a radio connectionthrough a radio network access such as Global System for Mobilcommunication (GSM), General Packet Radio Services (GPRS), Enhanced DataGSM Environment (EDGE), Wideband Code Division Multiple Access (WCDMA),among other communication standards. Network may include any wirelesscommunication mechanism by which information may travel between thedevices 504 and other computing devices in the network.

To ensure data transfer is secure, the computer systems 502, 504 and 506may transmit data via the network 508 using a variety of securitymeasures including TSL, SSL or VPN, among other security techniques.While the distributed computer system 500 illustrates three networkedcomputer systems, the distributed computer system 500 may include anynumber of computer systems, networked using any medium and communicationprotocol.

Various aspects and functions in accord with the present invention maybe implemented as specialized hardware or software executing in one ormore computer systems including the computer system 502 shown in FIG. 5.As depicted, the computer system 502 includes a processor 510, a memory512, a bus 514, an interface 516 and a storage system 518. The processor510, which may include one or more microprocessors or other types ofcontrollers, can perform a series of instructions that manipulate data.The processor 510 may be a well-known, commercially available processorsuch as an Intel Pentium, Intel Atom, ARM Processor, Motorola PowerPC,SGI MIPS, Sun UltraSPARC, or Hewlett-Packard PA-RISC processor, or maybe any other type of processor or controller as many other processorsand controllers are available. As shown, the processor 510 is connectedto other system placements, including a memory 512, by the bus 514.

The memory 512 may be used for storing programs and data duringoperation of the computer system 502. Thus, the memory 512 may be arelatively high performance, volatile, random access memory such as adynamic random access memory (DRAM) or static memory (SRAM). However,the memory 512 may include any device for storing data, such as a diskdrive or other non-volatile storage device, such as flash memory orphase-change memory (PCM). Various embodiments in accord with thepresent invention can organize the memory 512 into particularized and,in some cases, unique structures to perform the aspects and functionsdisclosed herein.

Components of the computer system 502 may be coupled by aninterconnection element such as the bus 514. The bus 514 may include oneor more physical busses (for example, busses between components that areintegrated within a same machine), and may include any communicationcoupling between system placements including specialized or standardcomputing bus technologies such as IDE, SCSI, PCI and InfiniBand. Thus,the bus 514 enables communications (for example, data and instructions)to be exchanged between system components of the computer system 502.

Computer system 502 also includes one or more interfaces 516 such asinput devices, output devices and combination input/output devices. Theinterface devices 516 may receive input, provide output, or both. Forexample, output devices may render information for externalpresentation. Input devices may accept information from externalsources. Examples of interface devices include, among others, keyboards,mouse devices, trackballs, microphones, touch screens, printing devices,display screens, speakers, network interface cards, etc. The interfacedevices 516 allow the computer system 502 to exchange information andcommunicate with external entities, such as users and other systems.

Storage system 518 may include a computer-readable andcomputer-writeable nonvolatile storage medium in which instructions arestored that define a program to be executed by the processor. Thestorage system 518 also may include information that is recorded, on orin, the medium, and this information may be processed by the program.More specifically, the information may be stored in one or more datastructures specifically configured to conserve storage space or increasedata exchange performance. The instructions may be persistently storedas encoded signals, and the instructions may cause a processor toperform any of the functions described herein. A medium that can be usedwith various embodiments may include, for example, optical disk,magnetic disk or flash memory, among others. In operation, the processor510 or some other controller may cause data to be read from thenonvolatile recording medium into another memory, such as the memory512, that allows for faster access to the information by the processor510 than does the storage medium included in the storage system 518. Thememory may be located in the storage system 518 or in the memory 512.The processor 510 may manipulate the data within the memory 512, andthen copy the data to the medium associated with the storage system 518after processing is completed. A variety of components may manage datamovement between the medium and the memory 512, and the invention is notlimited thereto.

Further, the invention is not limited to a particular memory system orstorage system. Although the computer system 502 is shown by way ofexample as one type of computer system upon which various aspects andfunctions in accord with the present invention may be practiced, aspectsof the invention are not limited to being implemented on the computersystem, shown in FIG. 5. Various aspects and functions in accord withthe present invention may be practiced on one or more computers havingdifferent architectures or components than that shown in FIG. 5. Forinstance, the computer system 502 may include specially-programmed,special-purpose hardware, such as for example, an application-specificintegrated circuit (ASIC) tailored to perform a particular operationdisclosed herein. Another embodiment may perform the same function usingseveral general-purpose computing devices running MAC OS System X withMotorola PowerPC processors and several specialized computing devicesrunning proprietary hardware and operating systems.

The computer system 502 may include an operating system that manages atleast a portion of the hardware placements included in computer system502. A processor or controller, such as processor 510, may execute anoperating system which may be, among others, a Windows-based operatingsystem (for example, Windows NT, Windows 2000/ME, Windows XP, Windows 7,or Windows Vista) available from the Microsoft Corporation, a MAC OSSystem X operating system available from Apple Computer, one of manyLinux-based operating system distributions (for example, the EnterpriseLinux operating system available from Red Hat Inc.), a Solaris operatingsystem available from Sun Microsystems, or a UNIX operating systemsavailable from various sources. Many other operating systems may beused, and embodiments are not limited to any particular operatingsystem.

The processor and operating system together define a computing platformfor which application programs in high-level programming languages maybe written. These component applications may be executable, intermediate(for example, C# or JAVA bytecode) or interpreted code which communicateover a communication network (for example, the Internet) using acommunication protocol (for example, TCP/IP). Similarly, functions inaccord with aspects of the present invention may be implemented using anobject-oriented programming language, such as SmallTalk, JAVA, C++, Ada,or C# (C-Sharp). Other object-oriented programming languages may also beused. Alternatively, procedural, scripting, or logical programminglanguages may be used.

Additionally, various functions in accord with aspects of the presentinvention may be implemented in a non-programmed environment (forexample, documents created in HTML, XML or other format that, whenviewed in a window of a browser program, render aspects of agraphical-user interface or perform other functions). Further, variousembodiments in accord with aspects of the present invention may beimplemented as programmed or non-programmed placements, or anycombination thereof. For example, a web page may be implemented usingHTML while a data object called from within the web page may be writtenin C++. Thus, the invention is not limited to a specific programminglanguage and any suitable programming language could also be used.

It is to be appreciated that embodiments of the methods and apparatusesdiscussed herein are not limited in application to the details ofconstruction and the arrangement of components set forth in thefollowing description or illustrated in the accompanying drawings. Themethods and apparatuses are capable of implementation in otherembodiments and of being practiced or of being carried out in variousways. Examples of specific implementations are provided herein forillustrative purposes only and are not intended to be limiting. Inparticular, acts, elements and features discussed in connection with anyone or more embodiments are not intended to be excluded from a similarrole in any other embodiments.

Example Web Site For Managing Genomic Testing Results

FIG. 32 illustrates an example site map 3200 for a genomic testingwebsite according to one embodiment. Site map 3200 details examples ofpages and transitions that are made available by the genomic testingwebsite. According to one embodiment, the website can be accessed via alogin page 3202. Once logged into the site, a user is directed to apatient index page 3204 (e.g., FIG. 6 illustrates an example indexpage). Selecting a patient from the index page directs the userinterface into a patient results summary and associated information page3206 (e.g., FIG. 7A-B illustrate an example results summary page).Selection of an information drawer with the information page allows theuser to expand the information displayed for each category. For example,the user can access expanded views for alterations 3208 (e.g., FIG. 7C-Dillustrate an expanded view of alterations), therapies 3210 (e.g., FIG.7I illustrates an example expanded therapy view), trials 3212 (e.g.,FIG. 7J illustrates an example trials expanded view), and references3214 (e.g., FIG. 7L illustrates an example references expanded view).

Selection within the expanded view causes a transition in the userinterface to a respective summary page. For example, selection withinthe alteration expanded view 3208 causes a transition to an alterationsummary page 3216 (e.g., FIG. 7E illustrates an example alterationsummary page). In another example, selection within the therapiesexpanded view 3210 causes a transition to a therapy summary page (e.g.,FIG. 7H illustrates an example therapy summary page). In anotherexample, selection within the trials expanded view transitions the userinterface to a trial summary page for the selected trial (e.g., FIG. 33illustrates an example trial summary page). In a further example,selection within the references expanded view transitions the userinterface to a reference summary view 3222 (e.g., FIG. 34 illustrates anexample reference summary view).

Views 3206-3214 are grouped into a patient report 3205. Additionalinformation can be made available in the report. For example, a legalinformation page 3224 can be accessed from the view of the report 3205.The legal information page 3224 can include information on thediagnostic purposes of the report and the genomic testing process. Theuser can also access information on terms of use of the site 3226 fromthe report page 3205.

FIGS. 8A and 8E show another example report page including links toupdates associated with the report page 3205. In one embodiment,selection of the updates transitions the user interface to an updatespage 3230 and including an updates timeline and associated informationview 3232 (e.g. FIG. 8B illustrates an example view of an updatestimeline and associated information page). The updates timeline view3232 can also be associated with expanded views including: alterationsexpanded view 3234 (e.g., FIG. 8B); therapies expanded view 3236; trialsexpanded view 3238; and references expanded view 3240. Each expandedview is associated with a respective summary page: alteration summarypage 3242; therapy summary page 3244; trial summary page 3246; andreference summary page 3248. Each summary includes links to an allupdates view including all summary page updates for a respectivecategory (e.g., 3250—all summary page updates, 3252—all therapy pageupdates, 3254—all trial page updates, and 3256 all reference pageupdates).

FIG. 32 shows a site map 3200 which provides access to system pages. Thesystem pages provide user access to account information 3260, userprofile information 3262, account members 3264, account settings 3266,and sign-out functions 3268. In addition, the user can access pages fordefining general user preferences, e.g., on system alerts (e.g., FIG. 35shows an example user interface for defining system alert preferencesgenerally and FIG. 36 shows an example user interface for definingalerts on a patient basis). The alerts setting pages can be used toaccess any alerts (e.g., 3270) for a user account, for example, at 3272.The site can also include pages for support 3274 and user feedback 3276.

FIG. 37 is a general framework design for an example user interface3700, according to one embodiment. At 3702, the UI can include a globalheader display. The global elements within the display can include username, alerts, support, and feedback. The global header can change basedon a user state. For example, if the user is logged in, the globalheader may display in a logged in state. In another example, if a useris not logged in the global header may display in a logged out state(e.g., eliminating the user name, account alerts, support and feedbackoptions). Other global elements can include a page title at 3704“Michael Thomas” and a breadcrumb trail at 3706 in a page header area3705. The breadcrumb trail can include links to previous pages traversedto arrive at a current view (e.g., 3700). In some embodiments, globalelements can be displayed to filter content view (e.g., shown in FIG. 6)depending on the content displayed. In other embodiments, the globalelements can include jump menus for navigating within the contentdisplayed on a page (e.g., at 3708). Upon accessing a specific patient,the patient's information can be displayed in a “report mode” indicatedat 3710. The report mode provides access to all information contained ina genomic test report. Where updated information associated with areport is available, an update icon is displayed at 3712.

The content that is displayed can be in a variety of formats. Examplecontent items are shown in FIG. 38. A patient index table 3802 can bedisplayed within a patient index view. In another example, displayedcontent can include an updates timeline view 3804. The updates timelineview can be organized and/or sorted based on information categories(e.g., interpretations—3806, therapies—3808, trials—3810, andreferences—3812). Rows within each information category can be displayedin as shown at 3814-3820. Each row can also include sort functionalityto enable sorting based on displayed columns (e.g., 3822A-C, 3824A-E,3826A-G, and 3828A-B).

FIG. 39 illustrates another example page accessible via a genomicreport. Page 3900 displays summary content (e.g., 3804 of FIG. 38)associated with an updates timeline 3902. At 3904 information categoryfilters may be engaged by selection within the user interface. Selectionof a category changes the display of the filters.

Information view in a report can be configured as accordion informationtables, where the accordion tables are responsive to selection to expandand display additional information within the table. FIG. 40 illustratesinformation in example views shown in an unexpanded or collapsed state.FIG. 41 illustrates information in example views shown in an expandedstate.

According to one embodiment, information update indicators can beglobally provided in views of user interface. FIG. 42 illustratesexample update indicators 4202—4214, which can be displayed withinrespective portions and/or screens of the user interface. Additionally,alert indicators can also be globally provided within views of the userinterface. FIG. 43 illustrates example alert indicators 4302-4306, whichcan be displayed different based on the type of alert. At 4302, acritical alert is displayed as an inline notification for infrequent andhigh priority alerts. At 4304, a high priority alert can be displayedwithin an information drawer. At 4306, an alert with a high frequencycan be displayed as an indicator within the information that has beenupdated (e.g., 4308).

The user interface can include multiple views of genomic information.FIG. 44 shows another embodiment of a test report view 4400. Page 4400can include a breadcrumb trail at 4402, update notifications 4404, testresults content 4406 (e.g., time stamp 4408, test description 4410,gene/alteration list 4412). An alternate initial view of a genomicreport is illustrated in FIG. 45, which can display information in acollapsed state as well as an expanded state (e.g., FIG. 46).

FIG. 47 illustrates an execution flow 4700 between respective pages of agenomic testing website. According to one embodiment, a user is invitedto access the genomic testing website at 4702, for example, via ane-mailed invitation. The user is brought to a registration input screen4704, and the registration information can be verified 4706. Onceverified, subsequent access to the genomic testing site allows the nowregistered user to login. For example, the user may access a login page4708 or login drawer 4710 to input their access information. Validaccess information allows the user to continue to a content landing page4712 or welcome screen. Alternatively, the user can accessadministrative functions (e.g., password reset request 4708A and receivea reset notification 4708B). Optionally the welcome screen can beomitted. From the content landing page, the user may access a list ofpatients 4714 (FIG. 6 illustrates an example patient list page) andassociated patient reports at 4716 (FIG. 7A illustrates an examplereport initial view). In some embodiments, alternative views of genomictest reports are available. For example, a full test results page 4718and view by alteration page 4720 can be accessed. FIG. 44 is an exampleof a full test results page. FIG. 45 is an example of a view byalteration page.

The information displayed in the report initial view 4716 providessummary information, for example, grouped by information categories(e.g., interpretations, trials, therapies, and references). Each groupof information can be accessed via the report initial view, to provideexpanded views of respective information responsive to selection by auser. For example, information in the report can be expanded to providean interpretation expanded view 4722 (e.g., shown in FIG. 7C); a trialsexpanded view 4724 (e.g., shown in FIG. 7I); a therapies expanded view4726 (e.g., shown in FIG. 7I); and a references expanded view 4728(e.g., shown in FIG. 7K). The alternative page views may also includeexpanded information views at 4730 (e.g., shown in FIG. 46).

The information displayed can be associated with respective summarypages providing additional information. For example, interpretationinformation items can be linked to a gene summary page 4732 (e.g., shownin FIG. 7E or 7F), a trial summary page 4734 (e.g., shown in FIG. 33), atherapy summary page 4736 (e.g., shown in FIG. 7G), and a referencesummary page 4738 (e.g., shown in FIG. 34). Each of the summary viewscan link back to their respective expanded view, and expanded views canbe collapsed to return to a report initial view 4716.

In some alternatives, upon accessing a report, the user may be directedto a report view with updates 4740. For example, if informationcontained in a patient report has changed since a last view, the systemcan provide a view of the patient report with update indicators. FIGS.8A and 8E illustrate an example interface with update indicators.Responsive to selection of an update indicator, an updates timeline page4742 can be displayed. FIG. 8B illustrates an example updates timelinepage. Like the report page, the update page can include expandable viewsof the update items. For example, selection of a trial category willexpand trial information into a trial expanded update view 4744. Invarious embodiments, selection of information items within view 4746transitions to a respective summary view associated with the selecteditem. For example, selection of specific trial information causes atransition to a display of a trial summary update page 4746.

Additionally, the user may access a summary of all available updates at4748. According to some embodiments, the site is configured to allow auser to access genomic information easily and interact with the genomicinformation at whatever level is desired. A quick review can be managedthrough initial report views and summary pages. Alternatively, detailedreview can be managed through the site via the summary pages availableon respective information sources and/or interactive access to detailedgenomic information. Further, the site facilitates access to newinformation through update indicators and access to pages specificallyorganizing updated information (e.g., 4740-4748).

In some embodiments, the site can also enable configuration of systembehavior through account set up pages (e.g., FIG. 48). For example, auser may access a profile page 4802 of FIG. 48 and edit theirinformation via profile editing page 4804 to define or edit profileinformation (e.g., profile image, contact information, background,etc.). A user can enable other users to access an account, for example,in a group practice setting. The user may access a people page 4806 todefine users and access rights (e.g., for accessing patient dataassociated with a particular practice). Further, the user can definebehavior settings for the site at 4808. For example, the user can definewhen and how the site provides alerts, information updates, etc. A usermay also access an alert drawer 4810 configured to provide access toalert information associated with an account. The user can access allavailable alerts via page 4812 by expanding the alerts drawer. Supportis available via page 4814, where the user may access supportinformation. Additionally, the user can provide feedback through afeedback drawer 4816.

According to some embodiments, the genomic testing site can also provideaccess to a genomic information community. In one embodiment, the siteprovides a community portal 4900 of FIG. 49 for accessing aggregatedgenomic testing information. Access to the community can start at aknowledge base portal page 4902 (FIG. 50 illustrates an exampleknowledge base page). The knowledge base page provides anonymizedinformation on genomic testing, patient populations, genes/alterations,therapies, trials, and/or reference information. Specific trialinformation can be accessed and/or searched at 4904 (shown in FIG. 51 isan example trial index page). Additional information on respectivetrials can be accessed via a trial summary page 4910.

Further, patient case study pages are made available in the communityportal. For example, patient case study pages can be accessed at 4906and reviewed for anonymized information on the patient, a diagnosis,tumor type, gene alteration, treatment notes, status of treatments,related patient case studies, related trials, and related references(discussed in greater detail below in FIG. 52). The community portal4900 may also provide access to community profiles. For example,participating users can identify their background, specialty, relatedusers (e.g., group practice), and activities within or out of thecommunity. The system can provide access to detailed community profilepages at 4910 (discussed in greater detail below in FIG. 53).

FIG. 50 illustrates an example knowledge base page 5000. The knowledgebase page 5000 can include information on aggregated and anonymizedgenomic test reports, patient populations, cancer diagnoses, etc. Forexample, at 5002 information can be displayed on: a number of patientcases, participating oncologist, participating medical professionals,cancers types researched, number of genes tested, number of identifiedalterations (e.g., via genomic testing reports), number of clinicaltrials, number of therapies, and number of references available toreview and/or discuss.

Page 5000 can include a number of options for navigating the informationin the community portal. For example, at 5004 a menu for navigatingwithin the available case studies is provided. Users can access casestudies based on matching condition information, including any one ormore of cancer, diagnosis, and genomic alteration. Further, options canbe provided for matching treatment information, or therapy and clinicaltrial information. In addition, options can be provided for matchingpatient characteristics, including age, sex, and diagnosis date. Otheroptions for accessing information in the knowledge base can also includekeyword search functions. For example, additional menus can provide fornavigation within the portal on cancer genomic information generally.Users can access information based on matching cancer type, specifiedgene, and specified alterations at 5006. Additionally, users can enterkeyword searches at 5006 to access matching information.

Page 5000 can also include summary information on discussion topicsbeing developed within the community portal. The information on thediscussion topics can be organized by categories, including, topic ofdiscussion, type, a number of notes in the discussion, and last post inthe discussion at 5008. A limited number of discussion topics can beshown in the knowledge base page 5000, with access to additional topicsprovided via links (e.g., “view all”).

Page 5000 can also provide information on the most discussed topicswithin the community. For example, at 5010 the most discussed topics aredisplayed for review. The most discussed topics can be limited in numberon the display at 5010, with access to additional topics available via a“view all” link. Page 5000 can also provide information on most viewedcase studies. For example, at 5012 page 5000 displays a list of the mostviewed case studies. For case studies that do not fit within the displayarea of 5012 remaining cased studies can be accessed via a “view all”option.

Other information can be displayed on page 5000 based on tracking useractivity within the community. For example, at 5014 displayed isinformation on recently open clinical trials. The information on therecently open clinical trial can include a description of the trial,diagnosis, and can include location information. In another example, at5016 a list of most recent publications is displayed. A “view all”option is available to access recent publications that do not fit withinthe display area of 5016.

The community portal can include additional pages for accessing moredetailed information. For example, the community portal can include aclinical trial page 5100, FIG. 51. Page 5100 can include menus forsearching available information on clinical trials. For example, at 5102users can enter keyword search criteria and/or access drop down menusfor targeted searching. Users can receive results on matching clinicaltrials by specifying study type, study result, conditions, andinterventions. Users can also filter matching clinical trials based onlocation, including, state and/or country. Matching trials can be shownin display area 5104. The resulting trials can be organized by studytitle, study conditions, study interventions, and trial status, forexample, within display area 5104. The available information (e.g.,matching clinical trials) can also be organized by pages to provideaccess to large numbers of clinical trials.

The community portal can also include detailed information on patientcase studies that contain anonymized patient outcome information(including, for example, as discussed with respect to systems andmethods for outcome tracking and analysis) and provide insight intoother oncologists' treatment paths and level of success. Page 5200 ofFIG. 52 illustrates an example patient case study made available throughthe community portal.

Anonymized information on the patent is provided at 5202 (e.g., via acase number) while providing non-identifying descriptive information(e.g., female, small cell lung cancer). The descriptive informationprovided can include age and sex, cancer type, primary tumor site—lung,current state of the cancer, diagnosis—metastatic carcinoma, anddiagnosis date (for example, shown at 5204). Patient case studies canalso provide genomic testing information associated with the patient.For example, the genomic testing on the patient's cancer identified sixalternations, and the respective alterations can be displayed at 5206.

For patients having treatment information, treatment notes can bedisplayed at 5208. The treatment information can be displayed at 5208and organized by attempted treatment, timeline for treatments, andstatus of treatment. In some examples, additional information can beavailable with each course of treatment (e.g., shown by an icondisplayed next to a treatment record). Additional information can alsobe displayed for patient treatment, including information on when a lastupdate occurred, and if a treatment change was indicated by the resultsof genomic testing (e.g., at 5210).

In addition to information on the patient, community comments and/ornotes can be displayed as part of a patient case study. For example,user comments can be displayed at 5212, and include any information arespective user wishes to share on the patient case study. Each commentcan include information on the posting member, which can be used toaccess a community profile (e.g., including background information,specialty information, etc.). Some users may suggest alternatetreatments and even provide links to other patient case studiesexploring the suggested treatments. Other users may post cautions and/orconsiderations, while other comments may specifically request feedbackfrom the community or request an answer to a question.

Information on the patient in the case study may also be augmented viarelated information displays. In one embodiment, the system can identifyand display related information with respect to the case study. Forexample, at 5214 links to related case studies can be displayed. At5216, links to related trials can also be displayed. The display ofrelated trials can be grouped on current status—closed or open. At 5218,related references can be displayed, and at 5220 related therapies canbe provided.

FIG. 53 shows an example user profile page 5300 accessible through thecommunity portal. According to one embodiment, a community participantcan define elements of a community profile for display. At 5302, theuser is identified, and the user identification can include informationon their profession, any specialty, and professional membership(s).Contact information can also be displayed to other community members at5304, and the user's background can be displayed (e.g., at 5306).

A user's community profile page 5300 can include activity informationtracking the user's recent activity within the community. At 5308, auser's recent posts, comments, interactions, shared reports, etc., canbe provided. Additional activity can be accessed via a “view more” link.Other physicians related to the user can also be displayed. For example,in a community profile display, members of a practice group can bedisplayed at 5310 as related members. When accessed by the user, theuser may edit their own profile via menu 5312.

According to some embodiments, various user interfaces are provided toenable users to access and comprehend genomic testing information. Theuser interfaces also make available community tools for collaborating onrelated cases, identifying relevant information, and enabling the bestinformation to be used by physician users to support their diagnoses.The system can also facilitate access to clinical trials and facilitatecommunication between clinical researchers and treating physicians.According to various embodiments, systems for managing genomic testingresults can be incorporated within systems for outcome tracking andanalysis. Additionally, the various embodiments, functions, and methodsdiscussed for outcome tracking and analysis can be incorporated withinembodiments of the systems and methods for managing genomic testingresults discussed herein. In some examples, genomic testing information(e.g., gene and alteration information) for patients can be associatedwith specific treatment and outcome information. In some examples,genomic test reports and dynamic displays can organize information onpatient outcome and treatment information. For example, a dynamicdisplay of genomic testing information can include references to outcomeand treatment information. In one instance, an outcome/treatment draweris provided to facilitate access to outcome and treatment information.In other examples, the outcome tracking and analysis system can be usedto request and provide access to genomic test results and associatedinformation.

According to another aspect, provided are systems and methods formanaging genomic testing information that provide a single reportingsource for accessing and applying available information on a patient'scancer. According to some embodiments, genomic testing on the patient'scancer provides specific information on the tumor, one or more genesimplicated by the tumor, and one or more alterations within the genes.The testing information on tumor, gene, and alteration can be used bythe system to manage delivery of curated information that focuses users(e.g., physicians) on actionable information within the genomic testinginformation. For example, publically available data (e.g., therapy data,clinical trial data, journal publications) can be interpreted to providethe curated information. The curated information can be accessed on thesystem based on its relationship to one or more of the tumor, gene, andalteration for a patient. The publically available information can alsobe processed on the system to provide navigable data structuresinforming the user of available actionable information associated with apatient's cancer.

In further aspects, the practitioner is able to view the single reportsource for genomic information on the system. The single report sourcecan incorporate tumor information, gene information, and genomicalteration information to review and, potentially, to apply actionablesteps towards treating various cancers. According to one embodiment, thesingle report source is dynamic, incorporating updates to any associatedinformation (e.g., new curated information, updated curated information,a new clinical trial, a new therapy, a new publication associated withany of an alteration, gene, tumor found in a genomic test report) asthey become available. The system can deliver update notificationsresponsive to new information. Further embodiments provide intuitivenavigation options within views on the system to expand the informationdisplayed and/or navigate to additional information on a selectedinformation source (e.g., specific information on a tumor, gene, and/oralteration, and external links to available information, among otheroptions).

According to one embodiment, a user interface is provided that allowseasy navigation to genomic alteration results and associated informationto reduce the amount of time necessary to determine an appropriatetreatment for a user. For instance, as a result of genomic testing, of apatient sample, particular genomic alterations may be detected anddisplayed to a user for a particular patient. The user may be presented,within the display, a collection of information that user would need toaccess to provide an informed treatment recommendation. For instance,with a first level view of identified alterations, the user may bepermitted to navigate to other information related to the genomicalterations, such as, therapy information, information on a clinicaltrial related to the genomic alteration, and any references that mightbe available to inform or support the application of such therapies. Byhaving such information within an easily navigable interface, users maymore quickly identify appropriate treatments.

According to one embodiment, the system may identify and display to theuser genomic alterations and associated information arranged based onactionability analysis. The actionability analysis can be configured todisplay genomic alteration and associated information having the highestdegree of actionability. In one embodiment, the actionability analysiscan prioritize information on available therapies or related therapiesover clinical trial information and available references. Additionally,the clinical trial information can be prioritized over availablereferences. The priority can be used by the system to define displayprecedence. For example, an order of display for genomic alterations andassociated information can reflect the priority and/or actionabilityanalysis.

In some embodiments, the system can provide an indication regarding thenumber or volume of therapy information items, the number or volume orclinical information items, and the number or volume of availablereference information items. The numbers within each group can also beused to establish priority. For example, on genomic alterations havingmultiple associate therapies, the alteration having the larger numbercan be displayed first. As updates to genomic alterations and associatedinformation occur, the actionability analysis can change over time toreflect the new information. Further, such updates can be communicateddirectly to the user and/or highlighted in a test report for the user'sreview.

According to another aspect, the system can be organized based on agenomic testing data model. In one embodiment, the data model isconfigured to organize information on tumor type, implicated geneswithin the tumor, and alteration types for the implicated genes forspecific tests and/or by patient. The system is configured to use thedata model to facilitate access to genomic alteration test results andall related information for a test and/or patient. In some embodiments,the gene/alteration combination can form at least part of the basis oforganization. Each gene/alteration combination can be linked in the datamodel to actionable information (if any exists). The actionableinformation can be linked to any of the gene/alteration combinations andcan optionally be match to the tumor type for a patient. Categorizationof all information in the data model by associating a gene, alteration,and/or tumor type provides insight into prescribed uses of therapies(on-label) and off-label applications based on related alterationinformation (e.g., information on different tumors but the samealteration—an effective therapy for the alteration in a different tumortype could be relevant to a patient's tumor type).

In some embodiments, users are able to share test reports and associatedinformation between physicians in a practice group or between physicianswithin an institution (e.g., hospital, treatment facility, etc.) Inaddition to the dynamic display of the genomic information andassociated information, some embodiments, of the system can provide forgeneration of physical and/or static reports. In one example, a physicalreport can be generated to include genomic alteration information for apatient and all the associated information organized into display groupsfor therapy, trial, and reference information.

According to one aspect, a system for managing delivery of genomictesting information is provided. The system comprises at least oneprocessor operatively connected to a memory, the at least one processorwhen executing is configured to access genomic testing results includingat least one gene and alteration combination for a patient's cancer,analyze one or more of a tumor type, gene, and alteration for thepatient's cancer, wherein analyzing includes identifying associatedinformation items matching at least one of the tumor type, gene, andalteration for the patient's cancer, and generate at least one genomicdata structure including at least one tag, wherein the at least one tagis selectable to transition a user interface from the genomic datastructure to an associated information display space including at leastone associated information item describing information related tocharacteristics of the genomic data structure.

In one embodiment, the system further comprises a user interfacecomponent, executed by the at least one processor, configured to displaythe at least one genomic data structure within a user interfaceaccessible over a communication network. In one embodiment, the userinterface component is configured to assign associated information itemsto categories responsive to a type of information for the associatedinformation item. In one embodiment, the user interface component isconfigured to generate two or more tags displayed within each genomicdata structure, wherein the two or more tags are selected from a groupof categories including therapy, clinical trial, genomic interpretation,and alteration. In one embodiment, the user interface component isconfigured to generate at least four tags within each genomic datastructure for at least the therapy, clinical trial, genomicinterpretation, and alteration categories.

In one embodiment, the user interface component is configured to displaya count of associated information items referenced by each tag. In oneembodiment, the user interface component is configured to highlight theat least one associated information item within the associatedinformation display space responsive to selection of the at least onetag. In one embodiment, the user interface component is configured togenerate at least one data structure in the associated informationdisplay space for organizing associated information items.

In one embodiment, the user interface component is configured to displaythe at least one organizing data structure in the associated informationdisplay space in an unexpanded view. In one embodiment, the unexpandedview conceals any associated information items. In one embodiment, theuser interface component is configured to display the at least oneorganizing data structure in an expanded view responsive to at least oneof the transition to the associated information space and selection ofthe at least one organizing data structure. In one embodiment, theexpanded view includes a display of the at least one associatedinformation organized by the at least one organizing data structure.

In one embodiment, the user interface component is configured togenerate organizing data structures for at least the therapy, clinicaltrial, genomic interpretation, alteration, and a references category. Inone embodiment, one organizing data structure organizes associatedinformation items for both the genomic interpretation and the alterationcategories. In one embodiment, the user interface component isconfigured to limit a number of organizing data structures displayed inthe expanded view. In one embodiment, the user interface component isconfigured to limit the number of organizing data structures displayedin the expanded view to one.

In one embodiment, the user interface component is configured togenerate an update organizing data structure for organizing any updatedassociated information items. In one embodiment, the user interfacecomponent is configured to identify updated associated information itemsresponsive to a last view date. In one embodiment, the user interfacecomponent is configured to display the at least one associatedinformation items within the associated information space.

In one embodiment, the user interface component is configured togenerate in each of the at least one associated information items aselectable display for navigating to at least one of a detailed view ofan associated information item and an external source for the at leastone information item. In one embodiment, the user interface component isconfigured to generate for each of the at least one associatedinformation items organized in the genomic interpretation category atleast one of: a) interpretive information, e.g., information of the roleof the gene in health and disease, e.g., in cancer, e.g., the patient'stype of cancer, or another cancer, including curated information e.g.,one or more identifiers of sources of primary information, e.g.,published journal articles, on the prevalence of the alteration inparticular cancers or populations, therapies for the subject genomicalteration, or related genomic alterations, clinical studies of specifictherapies for cancers within the current patient's tumor type orotherwise, and genomic alteration, e.g., a type of alteration, e.g.,amplification, deletion, translocation, etc.; b) the name of theaffected gene; and c) the type of alteration.

In one embodiment, the user interface component is configured togenerate for each of the at least one associated information itemsorganized in the therapy category one or more or all of: a) a therapy,e.g., a drug, one or more of all of: an indication of whether thetherapy is approved for the patient's tumor type; an indication ofwhether the therapy is approved for other tumor types (which can beuseful in identifying off-label uses); b) an identifier for a therapy;c) the identity of the gene involved in the alteration; and d) the typeof alteration. In one embodiment, the user interface component isconfigured to generate for each of the at least one associatedinformation items organized in the clinical trial category one or moreor all of the following (if there is such a clinical trial): a) anidentifier for a clinical trial, e.g., one that implicates one or moreor all of the patient's tumor type, a gene affected by the patient'salteration, the genetic alteration type; b) rationale for the trial,e.g., a statement of why the therapy is implicated in the patient'stumor type or another tumor type; c) a description of the trial, e.g.,an indication of phase, and type of cancer treated; d) a geographiclocation of trial; e) an identification of the target in clinical trial,e.g., aurora kinase, and wherein in embodiments, one or more or all, ofa, b, c and d, are presented concurrently to the user, without need forleaving the screen, e.g., without further computer operation or withoutmore than brief computer operation by the user.

In one embodiment, the user interface component is configured togenerate for each of the at least one associated information itemsorganized in the references category one or more or all of thefollowing: a) reference bibliography information e.g., author, title,publisher, location, copyright, journal name, journal title, publicationname, publication company, ISBN, etc.; and b) a navigable link to thereference.

In one embodiment, the system further comprises a storage componentexecuted by the at least one processor configured to organize genomictesting results and associated information by patient according to adata model. In one embodiment, the data model comprises a data structureassociated with patient records, and wherein the data structure includesdata records for specification of tumor type, gene, and alteration. Inone embodiment, all genomic testing results and the associatedinformation is accessible by the storage component using gene andalteration records. In one embodiment, each patient record includes geneand alteration data units, and the storage component is configured toassociate actionable information (e.g., therapy information items orclinical trial information items) to the gene and alteration date units.In one embodiment, the actionable information includes therapyinformation items that specify whether an associated therapy is approvedby the FDA in the patient's tumor type, and whether the associatedtherapy is approved by the FDA in another tumor type.

In one embodiment, the data model includes specification of anactionability evaluation for associated information items. In oneembodiment, therapy information items are assigned a highest level ofactionability. In one embodiment, clinical trial information items areassigned a second level of actionability. In one embodiment, referenceinformation items are assigned a lowest level of actionability. In oneembodiment, genomic data structures can be assigned a display precedenceresponsive to a level of actionability determined from respectiveassociated information items.

In one embodiment, the system further comprises an update component,executed by the at least one processor, configured to track any updatesto one or more of genomic test results and any associated informationitems. In one embodiment, the update component is configured tocommunicate update notification to users responsive to identification ofupdated information. In one embodiment, the update component isconfigured to generate notifications according to user notificationpreferences.

In one embodiment, the system further comprises a report componentconfigured to generate static reports containing all gene alterationcombinations specific to a patient and all associated information itemsorganized into respective display areas on the report, wherein therespective display areas are arranged by information type. In oneembodiment, the report component is configured to deliver the staticreport via a fax.

In one embodiment, the system further comprises a curation component,executed by the at least one processor, configured to identifyinformation sources relevant to any one or more of a patient's tumortype, at least one gene implicated by the tumor, and an alteration typefor the at least one gene. In one embodiment, the curation component isconfigured to generate interpretive statements accessible at least byusing a gene and alternation combination. In one embodiment, theinterpretive statement include e.g., information of the role of the genein health and disease, e.g., in cancer, e.g., the patient's type ofcancer, or another cancer, including curated information e.g., one ormore identifiers of sources of primary information, e.g., publishedjournal articles, on the prevalence of the alteration in particularcancers or populations, therapies for the subject genomic alteration, orrelated genomic alterations, clinical studies of specific therapies forcancers within the current patient's tumor type or otherwise, andgenomic alteration, e.g., a type of alteration, e.g., base substitution,insertion, deletion, amplification, homozygous deletion, rearrangement.

In one embodiment, the curation component is configured to categorizeinformation sources, and store the categorizations at least for use by auser interface component. In one embodiment, the curation component isconfigured to identify updates to treatment options. In one embodiment,the curation component is configured to identify updates genomicalteration interpretive statements. In one embodiment, the curationcomponent is configured to tag updated records responsive to at leastone of timing of a study, approval of a therapy, start of a new trial,and publication of a new reference.

According to one aspect, a computer implemented method for deliveringpatient information is provided. The method is comprised of: A)optionally, providing reports for a plurality of patients, e.g., aplurality of patients of a user; B) providing, e.g., displaying, e.g.,responsive to a selection by a user, a first portion of said report,said first portion comprising, one or more or all of: i) patientinformation comprising a) Patient Diagnosis; and, optionally, one ormore or all of b) Patient identifier; c) other Patient bibliographicinformation, e.g., age; and ii) a genomic alteration space, e.g., agenomic alteration brick, for each cancer cell genomic alteration, whichcomprises or provides, e.g., without further computer operation by theuser, one or more or all of: a) a first space, or cancer cell genomicalteration space, having, e.g., an indication of a gene involved; b) asecond space, or type of alteration space, having, e.g., an indicationof alteration type, e.g., an amplification, translocation, or pointmutation; c) a third space, or therapy or actionable item space; d) afourth space, or for clinical trial space; wherein in embodiments, oneor more or all, of a, b, c and d, are presented concurrently to theuser, without need for leaving the screen, e.g., without furthercomputer operation or without more than brief computer operation by theuser; and iii) an associated information space, comprising one or moreor all of: a) first associated space, or genomic alterationinterpretation space, e.g., a genomic alteration interpretation drawer,b) second associated space, or therapy space, e.g., a therapy drawer, c)third associated space, or clinical trial space, e.g., a clinical trialdrawer, d) forth associated space, or references space, e.g., areferences drawer, e) an optional fifth associated space, or updatesspace, e.g., an updates drawer, wherein in embodiments, one or more orall, of a, b, c and d, are presented in an unexpanded or expanded viewto the user, without need for leaving the screen, e.g., without furthercomputer operation for the unexpanded view and without more than briefcomputer operation by the user to transition to the expanded view; andC) providing or displaying, e.g., in response to user input, e.g., abrief computer operation, which selects one of B(2)a-d: i) for B(2) a orb, one or more or all of: a) interpretive information, e.g., informationof the role of the gene in health and disease, e.g., in cancer, e.g.,the patient's type of cancer, or another cancer, including curatedinformation e.g., one or more identifiers of sources of primaryinformation, e.g., published journal articles, on the prevalence of thealteration in particular cancers or populations, therapies for thesubject genomic alteration, or related genomic alterations, clinicalstudies of specific therapies for cancers within the current patient'stumor type or otherwise, and genomic alteration, e.g., a type ofalteration, e.g., amplification, deletion, translocation, etc.; b) thename of the affected gene; and c) the type of alteration; ii) for B(2)c, one or more or all of: a) a therapy, e.g., a drug, one or more of allof: an indication of whether the therapy is approved for the patient'stumor type; an indication of whether the therapy is approved for othertumor types (which can be useful in identifying off-label uses); b) anidentifier for a therapy; c) the identity of the gene involved in thealteration; and d) the type of alteration; iii) for B(2) d, one or moreor all of one or more of the following (if there is such a clinicaltrial): a) an identifier for a clinical trial, e.g., one that implicatesone or more or all of the patient's tumor type, a gene affected by thepatient's alteration, the genomic alteration type; b) rationale for thetrial, e.g., a statement of why the therapy is implicated in thepatient's tumor type or another tumor type; c) a description of thetrial, e.g., an indication of phase, and type of cancer treated; d)geographic location of trial; e) identification of the target inclinical trial, e.g., aurora kinase, wherein in embodiments, one or moreor all, of a, b, c and d, are presented concurrently to the user,without need for leaving the screen, e.g., without further computeroperation or without more than brief computer operation by the user.

In one embodiment, the method further comprises: D) providing ordisplaying, e.g., in response to user input, e.g., a brief computeroperation, which selects one of B(3)a-e: i) for B(3) a, one or more orall of: a) interpretive information, e.g., information of the role ofthe gene in health and disease, e.g., in cancer, e.g., the patient'stype of cancer, or another cancer, including curated information e.g.,one or more identifiers of sources of primary information, e.g.,published journal articles, on the prevalence of the alteration inparticular cancers or populations, therapies for the subject genomicalteration, or related genomic alterations, clinical studies of specifictherapies for cancers within a current patient's tumor type orotherwise, or related, genomic alteration; b) the name of the affectedgene; and c) the type of alteration; ii) for B(3) b, one or more or allof: a) a therapy, e.g., a drug, one or more of all of: an indication ofwhether the therapy is approved for the patient's tumor type; anindication of whether the therapy is approved for other tumor types(which can be useful in identifying off-label uses); b) an identifierfor a therapy; c) the identity of the gene involved in the alteration;and d) the type of alteration; iii) for B(3)c, one or more or all of oneor more of the following (if there is such a clinical trial): a) anidentifier for a clinical trial, e.g., one that implicates one or moreor all of the patient's tumor type, a gene affected by the patient'salteration, the genomic alteration type; b) rationale for the trial,e.g., a statement of why the therapy is implicated in the patient'stumor type or another tumor type; c) a description of the trial, e.g.,an indication of phase, and type of cancer treated; d) geographiclocation of trial; e) identification of the target in clinical trial,e.g., aurora kinase, iv) for B(3)d, one or more or all of the following:a) reference bibliography information e.g., author, title, publisher,location, copyright, journal name, journal title, publication name,publication company, ISBN, etc.; and b) a navigable link to thereference; v) for B(3)e, one or more or all of the following: a) anupdates time line including updated information for any one or more orall of D(1)-(4); wherein in embodiments, one or more or all, of a, b, c,d, and e, are presented consecutively to the user, without need forleaving the screen, without more than brief computer operation by theuser.

In one embodiment, the method includes successive execution of C), e.g.successive access, e.g., by brief computer operation, by a user to aplurality of genomic alteration spaces, e.g., bricks. In one embodiment,the method includes successive accesses, e.g., by brief computeroperation, by a user to a plurality of spaces selected within B(2)a-d.In one embodiment, the method includes selection of successiveoperations described above, by no more than y, wherein y is equal to orless than two, brief computer operations, for each of the plurality ofgenomic alteration spaces accessed.

In one embodiment, the method further comprises migration from the firstportion, through at least one of the genomic alteration spaces, e.g.,bricks, to the associated information space (e.g., the clinical trialspace, therapy space, interpretation space) by no more than X, wherein Xis equal to or less than one, brief computer operations. In oneembodiment, the method further comprises migration from the firstportion, through at least one of the genomic alteration spaces, e.g.,bricks, to the associated information space (e.g., the clinical trialspace, therapy space, interpretation space) by no more than X, wherein Xis equal to or less than two, brief computer operations.

In one embodiment, the method further comprises successive execution ofthe act of migrating from the first portion, through at least one of thegenomic alteration spaces, e.g., bricks, to the associated informationspace (e.g., the clinical trial space, therapy space, interpretationspace) Z times, wherein Z successive acts of migrating can be performedwith no more than z*x brief computer operations, wherein x is equal toone or two, or no more than z*x plus z. In one embodiment, C) isexecuted successively to access at least 1, 2, 3, 4, 5, 6, 7, 8, 9, or10, genomic alteration spaces, resulting in 1, 2, 4, 5, 6, 7, 8, 9, or10 successive transitions to the associated information space.

According to one aspect a computer implemented method for managingdelivery of genomic testing information is provided. The methodcomprises accessing, by a computer system, genomic testing resultsincluding at least one gene and alteration combination for a patient'scancer, analyzing, by the computer system, one or more of a tumor type,gene, and alteration for the patient's cancer, wherein analyzingincludes identifying associated information items matching at least oneof the tumor type, gene, and alteration for the patient's cancer, andgenerating, by the computer system, at least one genomic data structureincluding at least one tag for display in a user interface, wherein theat least one tag is selectable to transition the user interface from thegenomic data structure to an associated information display spaceincluding at least one associated information item describinginformation related to characteristics of the genomic data structure.

According to one embodiment, the method further comprises displaying, bythe computer system, the at least one genomic data structure within theuser interface accessible over a communication network. According to oneembodiment, the method further comprises assigning, by the computersystem, the associated information items to categories responsive to atype of information for a respective associated information item.According to one embodiment, the method further comprises generating, bythe computer system, two or more tags displayed within each genomic datastructure, wherein the two or more tags are selected from a group ofcategories including therapy, clinical trial, genomic interpretation,and alteration. According to one embodiment, the method furthercomprises generating, by the computer system, at least four tags withineach genomic data structure for at least the therapy, clinical trial,genomic interpretation, and alteration categories. According to oneembodiment, the method further comprises displaying, by the computersystem, a count of associated information items referenced by each tag.According to one embodiment, the method further comprises highlighting,by the computer system, the at least one associated information itemwithin the associated information display space responsive to selectionof the at least one tag.

According to one embodiment, the method further comprises generating, bythe computer system, at least one data structure in the associatedinformation display space for organizing associated information items.According to one embodiment, the method further comprises displaying, bythe computer system, the at least one organizing data structure in theassociated information display space in an unexpanded view. According toone embodiment, the unexpanded view conceals any associated informationitems.

According to one embodiment, the method further comprises displaying, bythe computer system, the at least one organizing data structure in anexpanded view responsive to at least one of the transition to theassociated information space and selection of the at least oneorganizing data structure. According to one embodiment, the expandedview includes a display of the at least one associated informationorganized by the at least one organizing data structure. According toone embodiment, the method further comprises generating, by the computersystem, organizing data structures for at least the therapy, clinicaltrial, genomic interpretation, alteration, and a references category.According to one embodiment, one organizing data structure organizesassociated information items for both the genomic interpretation and thealteration categories. According to one embodiment, the method furthercomprises limiting, by the computer system, a number of organizing datastructures displayed in the expanded view.

According to one embodiment, the method further comprises limiting, bythe computer system, the number of organizing data structures displayedin the expanded view to one. According to one embodiment, the methodfurther comprises generating, by the computer system, an updateorganizing data structure for organizing any updated associatedinformation items. According to one embodiment, the method furthercomprises identifying, by the computer system, updated associatedinformation items responsive to a last view date. According to oneembodiment, the method further comprises displaying, by the computersystem, the at least one associated information items within theassociated information space. According to one embodiment, the methodfurther comprises generating, by the computer system, in each of the atleast one associated information items a selectable display fornavigating to at least one of a detailed view of an associatedinformation item and an external source for the at least one informationitem.

According to one embodiment, the method further comprises generating, bythe computer system, for each of the at least one associated informationitems organized in the genomic interpretation category at least one of:a) interpretive information, e.g., information of the role of the genein health and disease, e.g., in cancer, e.g., the patient's type ofcancer, or another cancer, including curated information e.g., one ormore identifiers of sources of primary information, e.g., publishedjournal articles, on the prevalence of the alteration in particularcancers or populations, therapies for the subject genomic alteration, orrelated genomic alterations, clinical studies of specific therapies forcancers within the current patient's tumor type or otherwise, andgenomic alteration, e.g., a type of alteration, e.g., amplification,deletion, translocation, etc.; b) the name of the affected gene; and c)the type of alteration.

According to one embodiment, the method further comprises generating, bythe computer system, for each of the at least one associated informationitems organized in the therapy category one or more or all of: a) atherapy, e.g., a drug, one or more of all of: an indication of whetherthe therapy is approved for the patient's tumor type; an indication ofwhether the therapy is approved for other tumor types (which can beuseful in identifying off-label uses); b) an identifier for a therapy;c) the identity of the gene involved in the alteration; and d) the typeof alteration. According to one embodiment, the method further comprisesgenerating, by the computer system, for each of the at least oneassociated information items organized in the clinical trial categoryone or more or all of the following (if there is such a clinical trial):a) an identifier for a clinical trial, e.g., one that implicates one ormore or all of the patient's tumor type, a gene affected by thepatient's alteration, the genetic alteration type; b) rationale for thetrial, e.g., a statement of why the therapy is implicated in thepatient's tumor type or another tumor type; c) a description of thetrial, e.g., an indication of phase, and type of cancer treated; d) ageographic location of trial; e) an identification of the target inclinical trial, e.g., aurora kinase, and wherein in embodiments, one ormore or all, of a, b, c and d, are presented concurrently to the user,without need for leaving the screen, e.g., without further computeroperation or without more than brief computer operation by the user.

According to one embodiment, the method further comprises generating, bythe computer system, for each of the at least one associated informationitems organized in the references category one or more or all of thefollowing: a) reference bibliography information e.g., author, title,publisher, location, copyright, journal name, journal title, publicationname, publication company, ISBN, etc.; and b) a navigable link to thereference.

According to one embodiment, the method further comprises organizing, bythe computer system, genomic testing results and associated informationby patient according to a data model. According to one embodiment, themethod further comprises storing, by the computer system, a datastructure associated with patient records, and wherein the datastructure includes data records for specification of tumor type, gene,and alteration. According to one embodiment, all genomic testing resultsand the associated information is accessible by the computer systemusing gene or alteration records. According to one embodiment, eachpatient record includes gene and alteration data units, and the methodfurther comprises associating actionable information (e.g., therapyinformation items or clinical trial information items) to the gene andalteration date units. According to one embodiment, the actionableinformation includes therapy information items that specify whether anassociated therapy is approved by the FDA in the patient's tumor type,and whether the associated therapy is approved by the FDA in anothertumor type.

According to one embodiment, the data model includes specification of anactionability evaluation for associated information items. According toone embodiment, the method further comprises assigning, by the computersystem, a highest level of actionability to therapy information items.According to one embodiment, the method further comprises assigning, bythe computer system, a second level of actionability to clinical trialinformation items. According to one embodiment, the method furthercomprises, by the computer system, a lowest level of actionability toreference information items. According to one embodiment, the methodfurther comprises assigning, by the computer system, a displayprecedence responsive to a level of actionability determined fromrespective associated information items.

According to one embodiment, the method further comprises tracking, bythe computer system, any updates to one or more of genomic test resultsand any associated information items. According to one embodiment, themethod further comprises communicating, by the computer system, updatenotification to users responsive to identification of updatedinformation. According to one embodiment, the method further comprisesgenerating, by the computer system, notifications according to usernotification preferences.

According to one embodiment, the method further comprises generating, bythe computer system, static reports containing all gene alterationcombinations specific to a patient and all associated information itemsorganized into respective display areas on the report, wherein therespective display areas are arranged by information type. According toone embodiment, the method further comprises delivering, by the computersystem, the static report via a fax.

According to one embodiment, the method further comprises identifying,by the computer system, information sources relevant to any one or moreof a patient's tumor type, at least one gene implicated by the tumor,and an alteration type for the at least one gene. According to oneembodiment, the method further comprises generating, by the computersystem, interpretive statements accessible at least by using a gene andalternation combination. According to one embodiment, whereininterpretive statements include e.g., information of the role of thegene in health and disease, e.g., in cancer, e.g., the patient's type ofcancer, or another cancer, including curated information e.g., one ormore identifiers of sources of primary information, e.g., publishedjournal articles, on the prevalence of the alteration in particularcancers or populations, therapies for the subject genomic alteration, orrelated genomic alterations, clinical studies of specific therapies forcancers within the current patient's tumor type or otherwise, andgenomic alteration, e.g., a type of alteration, e.g., base substitution,insertion, deletion, amplification, homozygous deletion, rearrangement.

According to one embodiment, the method further comprises categorizing,by the computer system, information sources, and storing thecategorizations at least for use by a user interface component.According to one embodiment, the method further comprises identifying,by the computer system, updates to treatment options. According to oneembodiment, the method further comprises identifying, by the computersystem, updates genomic alteration interpretive statements. According toone embodiment, the method further comprises tagging, by the computersystem, updated records responsive to at least one of timing of a study,approval of a therapy, start of a new trial, and publication of a newreference.

According to one aspect, a system for delivering patient information isprovided. The system comprises at least one processor operativelyconnect to a memory, the at least one processor when executing causesthe system to perform operations for: A) optionally, providing reportsfor a plurality of patients, e.g., a plurality of patients of a user; B)providing, e.g., displaying, e.g., responsive to a selection by a user,a first portion of said report, said first portion comprising, one ormore or all of: i) patient information comprising a) Patient Diagnosis;and, optionally, one or more or all of b) Patient identifier; c) otherPatient bibliographic information, e.g., age; and ii) a genomicalteration space, e.g., a genomic alteration brick, for each cancer cellgenomic alteration, which comprises or provides, e.g., without furthercomputer operation by the user, one or more or all of: a) a first space,or cancer cell genomic alteration space, having, e.g., an indication ofa gene involved; b) a second space, or type of alteration space, having,e.g., an indication of alteration type, e.g., an amplification,translocation, or point mutation c) a third space, or therapy oractionable item space, d) a fourth space, or for clinical trial space,wherein in embodiments, one or more or all, of a, b, c and d, arepresented concurrently to the user, without need for leaving the screen,e.g., without further computer operation or without more than briefcomputer operation by the user; and iii) an associated informationspace, comprising one or more or all of: a) first associated space, orgenomic alteration interpretation space, e.g., a genomic alterationinterpretation drawer, b) second associated space, or therapy space,e.g., a therapy drawer; c) third associated space, or clinical trialspace, e.g., a clinical trial drawer, d) forth associated space, orreferences space, e.g., a references drawer, e) an optional fifthassociated space, or updates space, e.g., an updates drawer, wherein inembodiments, one or more or all, of a, b, c and d, are presented in anunexpanded or expanded view to the user, without need for leaving thescreen, e.g., without further computer operation for the unexpanded viewand without more than brief computer operation by the user to transitionto the expanded view; and C) providing or displaying, e.g., in responseto user input, e.g., a brief computer operation, which selects one ofB(2)a-d: i) for B(2) a or b, one or more or all of: a) interpretiveinformation, e.g., information of the role of the gene in health anddisease, e.g., in cancer, e.g., the patient's type of cancer, or anothercancer, including curated information e.g., one or more identifiers ofsources of primary information, e.g., published journal articles, on theprevalence of the alteration in particular cancers or populations,therapies for the subject genomic alteration, or related genomicalterations, clinical studies of specific therapies for cancers withinthe current patient's tumor type or otherwise, and genomic alteration,e.g., a type of alteration, e.g., amplification, deletion,translocation, etc.; b) the name of the affected gene; and c) the typeof alteration; ii) for B(2) c, one or more or all of: a) a therapy,e.g., a drug, one or more of all of: an indication of whether thetherapy is approved for the patient's tumor type; an indication ofwhether the therapy is approved for other tumor types (which can beuseful in identifying off-label uses); b) an identifier for a therapy;c) the identity of the gene involved in the alteration; and d) the typeof alteration; iii) for B(2) d, one or more or all of one or more of thefollowing (if there is such a clinical trial): a) an identifier for aclinical trial, e.g., one that implicates one or more or all of thepatient's tumor type, a gene affected by the patient's alteration, thegenomic alteration type; b) rationale for the trial, e.g., a statementof why the therapy is implicated in the patient's tumor type or anothertumor type; c) a description of the trial, e.g., an indication of phase,and type of cancer treated; d) geographic location of trial; e)identification of the target in clinical trial, e.g., aurora kinase,wherein in embodiments, one or more or all, of a, b, c and d, arepresented concurrently to the user, without need for leaving the screen,e.g., without further computer operation or without more than briefcomputer operation by the user.

According to one embodiment, the system is caused to perform operationsfor: D) providing or displaying, e.g., in response to user input, e.g.,a brief computer operation, which selects one of B(3)a-e: i) for B(3) a,one or more or all of: a) interpretive information, e.g., information ofthe role of the gene in health and disease, e.g., in cancer, e.g., thepatient's type of cancer, or another cancer, including curatedinformation e.g., one or more identifiers of sources of primaryinformation, e.g., published journal articles, on the prevalence of thealteration in particular cancers or populations, therapies for thesubject genomic alteration, or related genomic alterations, clinicalstudies of specific therapies for cancers within a current patient'stumor type or otherwise, or related, genomic alteration; b) the name ofthe affected gene; and c) the type of alteration; ii) for B(3) b, one ormore or all of: a) a therapy, e.g., a drug, one or more of all of: anindication of whether the therapy is approved for the patient's tumortype; an indication of whether the therapy is approved for other tumortypes (which can be useful in identifying off-label uses); b) anidentifier for a therapy; c) the identity of the gene involved in thealteration; and d) the type of alteration; iii) for B(3)c, one or moreor all of one or more of the following (if there is such a clinicaltrial): a) an identifier for a clinical trial, e.g., one that implicatesone or more or all of the patient's tumor type, a gene affected by thepatient's alteration, the genomic alteration type; b) rationale for thetrial, e.g., a statement of why the therapy is implicated in thepatient's tumor type or another tumor type; c) a description of thetrial, e.g., an indication of phase, and type of cancer treated; d)geographic location of trial; e) identification of the target inclinical trial, e.g., aurora kinase, iv) for B(3)d, one or more or allof the following: a) reference bibliography information e.g., author,title, publisher, location, copyright, journal name, journal title,publication name, publication company, ISBN, etc.; and b) a navigablelink to the reference; v) for B(3)e, one or more or all of thefollowing: a) an updates time line including updated information for anyone or more or all of D(1)-(4); wherein in embodiments, one or more orall, of a, b, c, d, and e, are presented consecutively to the user,without need for leaving the screen, without more than brief computeroperation by the user.

According to one embodiment, the system is caused to perform operationsfor successive execution of C), e.g. successive access, e.g., by briefcomputer operation, by a user to a plurality of genomic alterationspaces, e.g., bricks. According to one embodiment, the system is causedto perform operations for successive accesses, e.g., by brief computeroperation, by a user to a plurality of spaces selected within B(2)a-d.According to one embodiment, the system is caused to perform operationsfor selection of successive operations described in above, by no morethan y, wherein y is equal to or less than two, brief computeroperations, for each of the plurality of genomic alteration spacesaccessed. According to one embodiment, the system is caused to performoperations for migration from the first portion, through at least one ofthe genomic alteration spaces, e.g., bricks, to the associatedinformation space (e.g., the clinical trial space, therapy space,interpretation space) by no more than X, wherein X is equal to or lessthan one, brief computer operations.

According to one embodiment, the system is caused to perform operationsfor migration from the first portion, through at least one of thegenomic alteration spaces, e.g., bricks, to the associated informationspace (e.g., the clinical trial space, therapy space, interpretationspace) by no more than X, wherein X is equal to or less than two, briefcomputer operations. According to one embodiment, the system is causedto perform operations for successive execution of the act of migratingfrom the first portion, through at least one of the genomic alterationspaces, e.g., bricks, to the associated information space (e.g., theclinical trial space, therapy space, interpretation space) Z times,wherein Z successive acts of migrating can be performed with no morethan z*x brief computer operations, wherein x is equal to one or two, orno more than z*x plus z. According to one embodiment, C) is executedsuccessively by the system to access at least 56, 57, 58, 59, 60, 61,62, 63, 64, or 65, genomic alteration spaces, resulting in 56, 57, 59,60, 61, 62, 63, 64, or 10 successive transitions to the associatedinformation space.

According to one aspect, a computer-readable medium havingcomputer-readable signals stored thereon that define instructions that,as a result of being executed by a computer, instruct the computer toperform a method for managing delivery of genomic testing information isprovided. The method comprises accessing genomic testing resultsincluding at least one gene and alteration combination for a patient'scancer, analyzing one or more of a tumor type, gene, and alteration forthe patient's cancer, wherein analyzing includes identifying associatedinformation items matching at least one of the tumor type, gene, andalteration for the patient's cancer, and generating at least one genomicdata structure including at least one tag for display in a userinterface, wherein the at least one tag is selectable to transition theuser interface from the genomic data structure to an associatedinformation display space including at least one associated informationitem describing information related to characteristics of the genomicdata structure.

According to one embodiment, the method further comprises displaying theat least one genomic data structure within the user interface accessibleover a communication network. According to one embodiment, the methodfurther comprises assigning the associated information items tocategories responsive to a type of information for a respectiveassociated information item. According to one embodiment, the methodfurther comprises generating two or more tags displayed within eachgenomic data structure, wherein the two or more tags are selected from agroup of categories including therapy, clinical trial, genomicinterpretation, and alteration. According to one embodiment, the methodfurther comprises generating at least four tags within each genomic datastructure for at least the therapy, clinical trial, genomicinterpretation, and alteration categories. According to one embodiment,the method further comprises displaying a count of associatedinformation items referenced by each tag. According to one embodiment,the method further comprises highlighting the at least one associatedinformation item within the associated information display spaceresponsive to selection of the at least one tag.

According to one embodiment, the method further comprises generating atleast one data structure in the associated information display space fororganizing associated information items. According to one embodiment,the method further comprises displaying the at least one organizing datastructure in the associated information display space in an unexpandedview. According to one embodiment, the unexpanded view conceals anyassociated information items.

According to one embodiment, the method further comprises displaying theat least one organizing data structure in an expanded view responsive toat least one of the transition to the associated information space andselection of the at least one organizing data structure. According toone embodiment, the expanded view includes a display of the at least oneassociated information organized by the at least one organizing datastructure. According to one embodiment, the method further comprisesgenerating organizing data structures for at least the therapy, clinicaltrial, genomic interpretation, alteration, and a references category.According to one embodiment, one organizing data structure organizesassociated information items for both the genomic interpretation and thealteration categories. According to one embodiment, the method furthercomprises limiting a number of organizing data structures displayed inthe expanded view.

According to one embodiment, the method further comprises limiting thenumber of organizing data structures displayed in the expanded view toone. According to one embodiment, the method further comprisesgenerating an update organizing data structure for organizing anyupdated associated information items. According to one embodiment, themethod further comprises identifying updated associated informationitems responsive to a last view date. According to one embodiment, themethod further comprises displaying the at least one associatedinformation items within the associated information space. According toone embodiment, the method further comprises generating in each of theat least one associated information items a selectable display fornavigating to at least one of a detailed view of an associatedinformation item and an external source for the at least one informationitem.

According to one embodiment, the method further comprises generating foreach of the at least one associated information items organized in thegenomic interpretation category at least one of: a) interpretiveinformation, e.g., information of the role of the gene in health anddisease, e.g., in cancer, e.g., the patient's type of cancer, or anothercancer, including curated information e.g., one or more identifiers ofsources of primary information, e.g., published journal articles, on theprevalence of the alteration in particular cancers or populations,therapies for the subject genomic alteration, or related genomicalterations, clinical studies of specific therapies for cancers withinthe current patient's tumor type or otherwise, and genomic alteration,e.g., a type of alteration, e.g., amplification, deletion,translocation, etc.; b) the name of the affected gene; and c) the typeof alteration.

According to one embodiment, the method further comprises generating foreach of the at least one associated information items organized in thetherapy category one or more or all of: a) a therapy, e.g., a drug, oneor more of all of: an indication of whether the therapy is approved forthe patient's tumor type; an indication of whether the therapy isapproved for other tumor types (which can be useful in identifyingoff-label uses); b) an identifier for a therapy; c) the identity of thegene involved in the alteration; and d) the type of alteration.According to one embodiment, the method further comprises generating foreach of the at least one associated information items organized in theclinical trial category one or more or all of the following (if there issuch a clinical trial): a) an identifier for a clinical trial, e.g., onethat implicates one or more or all of the patient's tumor type, a geneaffected by the patient's alteration, the genetic alteration type; b)rationale for the trial, e.g., a statement of why the therapy isimplicated in the patient's tumor type or another tumor type; c) adescription of the trial, e.g., an indication of phase, and type ofcancer treated; d) a geographic location of trial; e) an identificationof the target in clinical trial, e.g., aurora kinase, and wherein inembodiments, one or more or all, of a, b, c and d, are presentedconcurrently to the user, without need for leaving the screen, e.g.,without further computer operation or without more than brief computeroperation by the user.

According to one embodiment, the method further comprises generating foreach of the at least one associated information items organized in thereferences category one or more or all of the following: a) referencebibliography information e.g., author, title, publisher, location,copyright, journal name, journal title, publication name, publicationcompany, ISBN, etc.; and b) a navigable link to the reference.

According to one embodiment, the method further comprises organizinggenomic testing results and associated information by patient accordingto a data model. According to one embodiment, the method furthercomprises storing a data structure associated with patient records, andwherein the data structure includes data records for specification oftumor type, gene, and alteration. According to one embodiment, allgenomic testing results and the associated information is accessible bythe computer system using gene or alteration records. According to oneembodiment, each patient record includes gene and alteration data units,and the method further comprises associating actionable information(e.g., therapy information items or clinical trial information items) tothe gene and alteration date units. According to one embodiment, theactionable information includes therapy information items that specifywhether an associated therapy is approved by the FDA in the patient'stumor type, and whether the associated therapy is approved by the FDA inanother tumor type.

According to one embodiment, the data model includes specification of anactionability evaluation for associated information items. According toone embodiment, the method further comprises assigning a highest levelof actionability to therapy information items. According to oneembodiment, the method further comprises assigning a second level ofactionability to clinical trial information items. According to oneembodiment, the method further comprises a lowest level of actionabilityto reference information items. According to one embodiment, the methodfurther comprises assigning a display precedence responsive to a levelof actionability determined from respective associated informationitems.

According to one embodiment, the method further comprises tracking anyupdates to one or more of genomic test results and any associatedinformation items. According to one embodiment, the method furthercomprises communicating update notification to users responsive toidentification of updated information. According to one embodiment, themethod further comprises generating notifications according to usernotification preferences.

According to one embodiment, the method further comprises generatingstatic reports containing all gene alteration combinations specific to apatient and all associated information items organized into respectivedisplay areas on the report, wherein the respective display areas arearranged by information type. According to one embodiment, the methodfurther comprises delivering the static report via a fax.

According to one embodiment, the method further comprises identifyinginformation sources relevant to any one or more of a patient's tumortype, at least one gene implicated by the tumor, and an alteration typefor the at least one gene. According to one embodiment, the methodfurther comprises generating interpretive statements accessible at leastby using a gene and alternation combination. According to oneembodiment, wherein interpretive statements include e.g., information ofthe role of the gene in health and disease, e.g., in cancer, e.g., thepatient's type of cancer, or another cancer, including curatedinformation e.g., one or more identifiers of sources of primaryinformation, e.g., published journal articles, on the prevalence of thealteration in particular cancers or populations, therapies for thesubject genomic alteration, or related genomic alterations, clinicalstudies of specific therapies for cancers within the current patient'stumor type or otherwise, and genomic alteration, e.g., a type ofalteration, e.g., base substitution, insertion, deletion, amplification,homozygous deletion, rearrangement.

According to one embodiment, the method further comprises categorizinginformation sources, and storing the categorizations at least for use bya user interface component. According to one embodiment, the methodfurther comprises identifying updates to treatment options. According toone embodiment, the method further comprises identifying updates genomicalteration interpretive statements. According to one embodiment, themethod further comprises tagging updated records responsive to at leastone of timing of a study, approval of a therapy, start of a new trial,and publication of a new reference.

According to one aspect, a computer-readable medium havingcomputer-readable signals stored thereon that define instructions that,as a result of being executed by a computer, instruct the computer toperform a method for delivering patient information is provided. Themethod is comprised of: A) optionally, providing reports for a pluralityof patients, e.g., a plurality of patients of a user; B) providing,e.g., displaying, e.g., responsive to a selection by a user, a firstportion of said report, said first portion comprising, one or more orall of: i) patient information comprising a) Patient Diagnosis; and,optionally, one or more or all of b) Patient identifier; c) otherPatient bibliographic information, e.g., age; and ii) a genomicalteration space, e.g., a genomic alteration brick, for each cancer cellgenomic alteration, which comprises or provides, e.g., without furthercomputer operation by the user, one or more or all of: a) a first space,or cancer cell genomic alteration space, having, e.g., an indication ofa gene involved; b) a second space, or type of alteration space, having,e.g., an indication of alteration type, e.g., an amplification,translocation, or point mutation; c) a third space, or therapy oractionable item space; d) a fourth space, or for clinical trial space;wherein in embodiments, one or more or all, of a, b, c and d, arepresented concurrently to the user, without need for leaving the screen,e.g., without further computer operation or without more than briefcomputer operation by the user; and iii) an associated informationspace, comprising one or more or all of: a) first associated space, orgenomic alteration interpretation space, e.g., a genomic alterationinterpretation drawer, b) second associated space, or therapy space,e.g., a therapy drawer, c) third associated space, or clinical trialspace, e.g., a clinical trial drawer, d) forth associated space, orreferences space, e.g., a references drawer, e) an optional fifthassociated space, or updates space, e.g., an updates drawer, wherein inembodiments, one or more or all, of a, b, c and d, are presented in anunexpanded or expanded view to the user, without need for leaving thescreen, e.g., without further computer operation for the unexpanded viewand without more than brief computer operation by the user to transitionto the expanded view; and C) providing or displaying, e.g., in responseto user input, e.g., a brief computer operation, which selects one ofB(2)a-d: i) for B(2) a or b, one or more or all of: a) interpretiveinformation, e.g., information of the role of the gene in health anddisease, e.g., in cancer, e.g., the patient's type of cancer, or anothercancer, including curated information e.g., one or more identifiers ofsources of primary information, e.g., published journal articles, on theprevalence of the alteration in particular cancers or populations,therapies for the subject genomic alteration, or related genomicalterations, clinical studies of specific therapies for cancers withinthe current patient's tumor type or otherwise, and genomic alteration,e.g., a type of alteration, e.g., amplification, deletion,translocation, etc.; b) the name of the affected gene; and c) the typeof alteration; ii) for B(2) c, one or more or all of: a) a therapy,e.g., a drug, one or more of all of: an indication of whether thetherapy is approved for the patient's tumor type; an indication ofwhether the therapy is approved for other tumor types (which can beuseful in identifying off-label uses); b) an identifier for a therapy;c) the identity of the gene involved in the alteration; and d) the typeof alteration; iii) for B(2) d, one or more or all of one or more of thefollowing (if there is such a clinical trial): a) an identifier for aclinical trial, e.g., one that implicates one or more or all of thepatient's tumor type, a gene affected by the patient's alteration, thegenomic alteration type; b) rationale for the trial, e.g., a statementof why the therapy is implicated in the patient's tumor type or anothertumor type; c) a description of the trial, e.g., an indication of phase,and type of cancer treated; d) geographic location of trial; e)identification of the target in clinical trial, e.g., aurora kinase,wherein in embodiments, one or more or all, of a, b, c and d, arepresented concurrently to the user, without need for leaving the screen,e.g., without further computer operation or without more than briefcomputer operation by the user.

In one embodiment, the method further comprises: D) providing ordisplaying, e.g., in response to user input, e.g., a brief computeroperation, which selects one of B(3)a-e: i) for B(3) a, one or more orall of: a) interpretive information, e.g., information of the role ofthe gene in health and disease, e.g., in cancer, e.g., the patient'stype of cancer, or another cancer, including curated information e.g.,one or more identifiers of sources of primary information, e.g.,published journal articles, on the prevalence of the alteration inparticular cancers or populations, therapies for the subject genomicalteration, or related genomic alterations, clinical studies of specifictherapies for cancers within a current patient's tumor type orotherwise, or related, genomic alteration; b) the name of the affectedgene; and c) the type of alteration; ii) for B(3) b, one or more or allof: a) a therapy, e.g., a drug, one or more of all of: an indication ofwhether the therapy is approved for the patient's tumor type; anindication of whether the therapy is approved for other tumor types(which can be useful in identifying off-label uses); b) an identifierfor a therapy; c) the identity of the gene involved in the alteration;and d) the type of alteration; iii) for B(3)c, one or more or all of oneor more of the following (if there is such a clinical trial): a) anidentifier for a clinical trial, e.g., one that implicates one or moreor all of the patient's tumor type, a gene affected by the patient'salteration, the genomic alteration type; b) rationale for the trial,e.g., a statement of why the therapy is implicated in the patient'stumor type or another tumor type; c) a description of the trial, e.g.,an indication of phase, and type of cancer treated; d) geographiclocation of trial; e) identification of the target in clinical trial,e.g., aurora kinase, iv) for B(3)d, one or more or all of the following:a) reference bibliography information e.g., author, title, publisher,location, copyright, journal name, journal title, publication name,publication company, ISBN, etc.; and b) a navigable link to thereference; v) for B(3)e, one or more or all of the following: a) anupdates time line including updated information for any one or more orall of D(1)-(4); wherein in embodiments, one or more or all, of a, b, c,d, and e, are presented consecutively to the user, without need forleaving the screen, without more than brief computer operation by theuser.

In one embodiment, the method includes successive execution of C), e.g.successive access, e.g., by brief computer operation, by a user to aplurality of genomic alteration spaces, e.g., bricks. In one embodiment,the method includes successive accesses, e.g., by brief computeroperation, by a user to a plurality of spaces selected within B(2)a-d.In one embodiment, the method includes selection of successiveoperations described above, by no more than y, wherein y is equal to orless than two, brief computer operations, for each of the plurality ofgenomic alteration spaces accessed.

In one embodiment, the method further comprises migration from the firstportion, through at least one of the genomic alteration spaces, e.g.,bricks, to the associated information space (e.g., the clinical trialspace, therapy space, interpretation space) by no more than X, wherein Xis equal to or less than one, brief computer operations. In oneembodiment, the method further comprises migration from the firstportion, through at least one of the genomic alteration spaces, e.g.,bricks, to the associated information space (e.g., the clinical trialspace, therapy space, interpretation space) by no more than X, wherein Xis equal to or less than two, brief computer operations.

In one embodiment, the method further comprises successive execution ofthe act of migrating from the first portion, through at least one of thegenomic alteration spaces, e.g., bricks, to the associated informationspace (e.g., the clinical trial space, therapy space, interpretationspace) Z times, wherein Z successive acts of migrating can be performedwith no more than z*x brief computer operations, wherein x is equal toone or two, or no more than z*x plus z. In one embodiment, C) isexecuted successively to access at least 1, 2, 3, 4, 5, 6, 7, 8, 9, or10, genomic alteration spaces, resulting in 1, 2, 4, 5, 6, 7, 8, 9, or10 successive transitions to the associated information space. It is tobe appreciated that embodiments of the methods and apparatuses discussedherein are not limited in application to the details of construction andthe arrangement of components set forth in the following description orillustrated in the accompanying drawings. The methods and apparatusesare capable of implementation in other embodiments and of beingpracticed or of being carried out in various ways. Examples of specificimplementations are provided herein for illustrative purposes only andare not intended to be limiting. In particular, acts, elements andfeatures discussed in connection with any one or more embodiments arenot intended to be excluded from a similar role in any otherembodiments.

Also, the phraseology and terminology used herein is for the purpose ofdescription and should not be regarded as limiting. Any references toembodiments or elements or acts of the systems and methods hereinreferred to in the singular may also embrace embodiments including aplurality of these elements, and any references in plural to anyembodiment or element or act herein may also embrace embodimentsincluding only a single element. References in the singular or pluralform are not intended to limit the presently disclosed systems ormethods, their components, acts, or elements. The use herein of“including,” “comprising,” “having,” “containing,” “involving,” andvariations thereof is meant to encompass the items listed thereafter andequivalents thereof as well as additional items. References to “or” maybe construed as inclusive so that any terms described using “or” mayindicate any of a single, more than one, and all of the described terms.Any references to front and back, left and right, top and bottom, upperand lower, and vertical and horizontal are intended for convenience ofdescription, not to limit the present systems and methods or theircomponents to any one positional or spatial orientation.

Having thus described several aspects of at least one embodiment of thisinvention, it is to be appreciated that various alterations,modifications, and improvements will readily occur to those skilled inthe art. Such alterations, modifications, and improvements are intendedto be part of this disclosure, and are intended to be within the spiritand scope of the invention. Accordingly, the foregoing description anddrawings are by way of example only.

What is claimed is:
 1. A system for tracking and analysis of cancertreatment and outcome information, the system comprising: at least oneprocessor operatively connected to a memory, the at least one processorwhen executing is configured to: receive treatment and outcomeinformation associated with a patient from at least one user; organizethe treatment and the outcome information according to one or more ofalteration, affected gene, affected pathway, tumor type, and treatment;generate outcome summary information including course of treatmentdisplays over time; and communicate the outcome summary information tothe at least one user.
 2. The system according to claim 1, wherein thetreatment information includes any one or more of drugs, therapeutics,named drugs, named therapeutics, drug cocktails, drug combinations,radiation, and surgery.
 3. The system according to claim 1, wherein theoutcome information includes information regarding a status of apatient's cancer.
 4. The system according to claim 3, wherein the statusof the patient's cancer includes one or more of complete response,partial response, stable disease, and progressive disease.
 5. The systemaccording to claim 1, wherein the course of treatment includesinformation regarding how patient is responding to treatment over time.6. The system according to claim 1, further comprising an analysiscomponent executed by the at least one processor configured to identifysimilar patients based on information related to genomic alteration. 7.The system according to claim 1, further comprising an analysiscomponent executed by the at least one processor configured to identifysimilar patients based on information related to affected geneidentified in a cancer.
 8. The system according to claim 1, furthercomprising an analysis component executed by the at least one processorconfigured to identify similar patients based on information related totreatment.
 9. The system according to claim 1, further comprising ananalysis component executed by the at least one processor configured toidentify similar patients based on related to tumor type.
 10. The systemaccording to claim 1, further comprising an analysis component executedby the at least one processor configured to identify similar patientsbased on information relating to a combination of at least two or moreof a group comprising alteration, affected gene, affected pathway, tumortype, and treatment.
 11. The system according to claim 1, furthercomprising an analysis component executed by the at least one processorconfigured to identify similar patients based on information related toat least one of alteration, affected gene, affected pathway, tumor type,and treatment for a patient's cancer, wherein the analysis component isconfigured to aggregate responsive information according to one or moreof alteration, affected gene, affected pathway, tumor type, andtreatment.
 12. The system according to claim 11, wherein the analysiscomponent is configured to aggregate similar patients within classes ofgenomic alterations.
 13. The system according to claim 12, wherein theclasses of genomic alterations include alterations in a specified domainof a gene.
 14. The system according to claim 13, wherein the domainincludes at least a kinase domain of the gene.
 15. The system accordingto claim 14, wherein the gene includes BRAF, and the specific domainsinclude at least one of kinase, BRAF V600E, and BRAF V600K.
 16. Thesystem according to claim 11, wherein the analysis component isconfigured to aggregate alteration information according to pathwaysaffected by respective alterations.
 17. The system according to claim11, where the analysis component is configured to aggregate similarpatient information based on functional similarity of identifiedalterations, which can be determined for distinct mutations havingfunctionally similar characteristics in the cancer cells. 18-25.(canceled)
 26. The system according to claim 1, further comprising ananalysis component executed by the at least one processor configured tocompare a current patient record to existing treatment information. 27.The system according to claim 26, wherein the existing treatmentinformation includes at least one of alteration, affected gene, affectedpathway, tumor type, and one or more treatments.
 28. The systemaccording to claim 27, wherein the analysis component is configured toidentify similar patients based on information in the current patientrecord, wherein identifying the similar patients includes determining amatch between the current patient record and at least one of alteration,affected gene, affected pathway, tumor type, and treatment.
 29. Thesystem according to claim 1, further comprising an analysis componentexecuted by the at least one processor configured to identify similarpatients based on user selection of at least one of tumor type,alteration, affected gene, and treatment.
 30. The system according toclaim 29, wherein the analysis component is configured to filter agrouping of similar patients based on additional specification of atleast one of alteration, affected gene, affected pathway, tumor type,and treatment. 31-48. (canceled)
 49. A computer implemented method fortracking and analysis of cancer treatment and outcome information, themethod comprising: receiving, by a computer system, treatment andoutcome information associated with a patient from at least one user;organizing, by the computer system, the treatment and the outcomeinformation according to one or more of alteration, affected gene,affected pathway, tumor type, and treatment; generating, by the computersystem, outcome summary information including course of treatmentdisplays over time; and communicating, by the computer system, theoutcome summary information to the at least one user.
 50. The methodaccording to claim 49, wherein the treatment information includes anyone or more of drugs, therapeutics, named drugs, named therapeutics,drug cocktails, drug combinations, radiation, and surgery.
 51. Themethod according to claim 49, wherein the outcome information includesinformation regarding a status of a patient's cancer.
 52. The methodaccording to claim 51, wherein the status of the patient's cancerincludes one or more of complete response, partial response, stabledisease, and progressive disease.
 53. The method according to claim 49,wherein the course of treatment includes information regarding howpatient is responding to treatment.
 54. The method according to claim49, further comprising identifying, by the computer system, similarpatients based on information related to genomic alteration.
 55. Themethod according to claim 49, further comprising identifying, by thecomputer system, similar patients based on information related toaffected gene identified in a cancer.
 56. The method according to claim49, further comprising identifying, by the computer system, similarpatients based on information related to treatment.
 57. The methodaccording to claim 49, further comprising identifying, by the computersystem, similar patients based on related to tumor type.
 58. The methodaccording to claim 49, further comprising identifying, by the computersystem, similar patients based on information relating to a combinationof at least two or more of a group comprising alteration, affected gene,affected pathway, tumor type, and treatment.
 59. The method according toclaim 49, further comprising: identifying, by the computer system,similar patients based on information related to at least one ofalteration, affected gene, affected pathway, tumor type, and treatmentfor a patient's cancer; and aggregating, by the computer system,responsive information according to one or more of alteration, affectedgene, affected pathway, tumor type, and treatment.
 60. The methodaccording to claim 59, further comprising aggregating, by the computersystem, similar patients within classes of alterations.
 61. The methodaccording to claim 60, wherein the classes of alteration includealterations in a specified domain of a gene.
 62. The method according toclaim 61, wherein the domain includes at least a kinase domain of thegene.
 63. The method according to claim 62, wherein the gene includesBRAF, and the specific domains include at least one of kinase, BRAFV600E, and BRAF V600K.
 64. The method according to claim 59, furthercomprising aggregating, by the computer system, alteration informationaccording to pathways affected by respective alterations.
 65. The methodaccording to claim 59, further comprising aggregating, by the computersystem, similar patient information based on functional similarity ofidentified alterations, which can be determined for distinct mutationshaving functionally similar characteristics in the cancer cells. 66-73.(canceled)
 74. The method according to claim 49, further comprisingcomparing, by the computer system, a current patient record to existingtreatment information.
 75. The method according to claim 74, wherein theexisting treatment information includes at least one of alteration,affected gene, affected pathway, tumor type, and one or more treatments.76. The method according to claim 74, further comprising identifying, bythe computer system, similar patients based on information in thecurrent patient record, wherein identifying the similar patientsincludes determining a match between the current patient record and atleast one of alteration, affected gene, affected pathway, tumor type,and treatment.
 77. The method according to claim 49, further comprisingidentifying, by the computer system, similar patients based on userselection of at least one of tumor type, alteration, genes, andtreatment.
 78. The method according to claim 77, further comprisingfiltering, by the computer system, a grouping of similar patients basedon additional specification of at least one of alteration, affectedgene, affected pathway, tumor type, and treatment. 79-96. (canceled) 97.The system according to claim 13, wherein the domain includes at leastan ATP binding pocket domain.
 98. The system according to claim 97,where the analysis component is configured to aggregate informationassociated with patients having at least one alteration within the ATPbinding pocket domain.
 99. The system according to claim 98, wherein theanalysis component is configured to aggregate information associatedwith patients having at least one alteration within the ATP bindingpocket domain for a specified gene.
 100. The system according to claim98, wherein the analysis component is configured to aggregationinformation associated with patients having at least one alterationwithin the ATP binding pocket domain for a plurality of genes.
 101. Thesystem according to claim 12, wherein the classes of alterationsincludes at least a tumor suppressor gene alteration class.
 102. Thesystem according to claim 101, wherein the analysis component isconfigured to aggregate the responsive information based on patientshaving at least one alteration within the tumor suppressor genealteration class.
 103. The system according to claim 102, wherein theanalysis component is configured to aggregate the responsive informationbased on a specific gene.
 104. The system according to claim 103,wherein the analysis component is configured to aggregate the responsiveinformation based on a plurality of specified genes.
 105. The systemaccording to claim 11, wherein the analysis component is configured toaggregate the responsive information based on at least one geneidentified within a pathway.
 106. The system according to claim 105,wherein the analysis component is configured to aggregate the responsiveinformation based on a plurality of genes identified within the pathway.107. The system according to claim 1, wherein the system is configuredto access or receive anonymized patient data from a plurality of datasources, and wherein the system further comprises an analysis componentexecuted by the at least one processor configured to identify similarpatients to a current patient based on information on the currentpatient's cancer.